Where do they stay during the day

Because you've had fighting issues in the past and one of the dogs is still a pup, I think separate kennel runs or separate areas of the house would be a great idea.

My two girls have run of the main part of our house during the day, but when we had a single tussle at one point I left them in separate rooms for about a month when I couldn't supervise.  Now we've worked back up to them being left out since we've had no issues since, but I make sure all bones are put up before I leave.

When my pup is trustworthy, I'll likely give him run of another room from the girls solely because he can be an obnoxious brat with them and they usually prefer to hang out on the couch during the day, so why rock that boat?  He's currently crated in another room to keep them from teasing him lol.

 I dont work but here's what I do when I leave the house. Use crates. I have 5 dogs.

My 8 year old mix breed and my 3 year old Irish Setter can be left out in the house. My 2 year old Chihuahua gets mad when left home and would pee in the house even if I was just gone for an hour. And I know she is housetrained. So she is crated. My 2 boys who are a year old will always be crated. They are my show dogs though so they have to be used to being crated. My Vizsla is good in the house when I am home but no way would I trust him alone in the house. My male Irish Setter is horrible still in the house so he only has one room he's allowed loose in. It works for me. All my dogs get lots of exercise even the Chihuahua.

Brooke is free in the house and trusted dosen't even own a crate.   Hailie when we are not home is crated, at night not.   and River is always crated at night and when we are not home.

I use a Dog Exercise Pen like the one below, not to small to be that tightly but big enough to move around. Leaving them free  and unsupervised when the puppy wants to wrestle the mix is a good call to start saving for a vet visit. One of the best investments i ever made

Brownie my 9 year old Beagle has free run of the house except we close our bedroom doors so he doesnt jump on our beds. Cuddles my 7 year old Cocker Spaniel is in the closed off kitchen. And, Lion, my 9 year old Newfie/Black Lab mix has free run of the house.

My dogs have the run of the house when I'm at work during the day.  They get exercised heavily before I leave in the am (except my Yorkie, who is 20, and doesn't care to come out of the linen closet except to pee and eat).  Everyone is trustworthy, and they each have their own couch;-)  TV and A/C (or pellet stove in winter) stay on all day for their comfort. 

Gaci and Shimmer stay in the bedroom, but with free room priveleges and freedom to move around. They could be trusted with free access to the house, but I rest more easily knowing they are safe there, and besides Gaci doesn't need to try to make a career out of watchdog barking the livingroom window.

Shimmer stays in a wire kennel (large dog size) in the bedroom. She will never have free access to the house.

Aspen stays in a kennel in the basement. Firstly, because we rent and if he ever got out he would likely be quite destructive on his own (he's my foster who is going through some training!!!), and secondly, it just is a second barrier (three doors separate them) between him and my guys when I'm not home.

Every dog I live with I go on an as-needed basis, based upon training and safety issues that may arise.

 Emma and Ena Bean are crated, in large crates, when I leave them. Jewel has an ex pen, because she isn't comfortable with being crated. Her ex pen has a top, because she can leap about 68256894 feet, straight up, with no effort. Everybody happily hops into their "kennel" when I'm getting ready to leave. They know treats are coming!

 I only have the one dog, Tootsie and she has free run of the apartment. She goes to my parents everyday while I work, so on the weekends if I leave its never more than 6 hours.

I can trust the mix to have the run of the house during the day, so it would be possible to just confine the puppy to the garage and leave the mix in the living room. I notice many of you do something similar with no issues.

Will I be setting myself up for territory or ownership issues when I give one dog the family's space but the other is confined to the garage, though? I need to be very careful with these guys not to allow any resource guarding, and allowing one to take ownership of anything non-trivial could set me up for trouble in that department.

Fenris

I can trust the mix to have the run of the house during the day, so it would be possible to just confine the puppy to the garage and leave the mix in the living room. I notice many of you do something similar with no issues.

Will I be setting myself up for territory or ownership issues when I give one dog the family's space but the other is confined to the garage, though? I need to be very careful with these guys not to allow any resource guarding, and allowing one to take ownership of anything non-trivial could set me up for trouble in that department.

Hmmm....a few things come to mind. I got my current dog, a little Pit when he was 9 months old.  He had never lived inside before and I was prepared that he would at least try to take a bite at the leather couches, but nothing and he is now two.  So IMO his serious and unsafe introduction to the world taught him to understand safety and I think that gave me the opportunity to give him things one thing at a time. 

My Bullmastiff, on the other hand, came to me when he was eight weeks old. I first met him when he was two and a half weeks old; took a two day trip to meet him and saw that he was born into a wonderful home. I then flew him home to me when he was eight weeks old.  I was assured that he would be fine in the crate, it was only a couple of hours by plane etc.  Well...he _ _ _ _ all over his crate and he was covered in it.  I was crying with joy to receive him and laughing at the smell and the sight of him. I just held him, stinky as he was, while my faithful sister did what she could to disassemble the crate without getting too much on her. 

Once home, this much nurtured little entity tried to eat or chew glass table tops, plants .... dining room chair legs and cross pieces were his specialty .  Bottom line is that he was a real handful to keep tabs on...no toys, no sour or foul sprays did the trick.  We worked every day until he finally got it. I crated him when I went to work and checked on him at lunch.  When he was almost a year old,  I thought it was time to spring him from the crate.  This was a good thing until one day I came home and he had hit the bottom shelves of the library in my office.  Videos, books....plastic, video springs and paper everywhere....so we went back to crating for awhile.   The bottom line is that a one year old Bullmastiff can still be really goofy so you are wise to continue to confine him.

I think your thoughts around letting the older dog remain in the house and putting the Bully in the garage is good. I would also suggest that your concern regarding territory is a good one...so maybe try alternating things a bit.  If your Bully isn't fully trustworthy loose in the house...leave him crated in the house when you are only going to be out for short periods (shopping etc.)...and put the GSD in the garage.  Alternatively, let the older dog have the roam of the house when you are gone for long periods of time and put the Bully in the garage...while sitll keeping the area safe and secure.

I'm not sure how much of a sense of time dogs have and I think when they are alone they sleep most of the time...so I don't think that when it comes to two, four or eight hours...it will reverse the positive effects of the fact that they are being alternated so they should come to understand that they are sharing territory.

Good luck....

Thanks for the advice! I hadn't thought of rotating. We have kids, which makes life busy, which means lots of times when we need to run errands, take kids to activities, go to a movie, all that stuff.

One hour here, two hours here. The puppy can be trusted for that long in the house, just not much longer. Just like your bully, she'll eat the house or leave puddles. House trained, yes, but she's still young enough to have accidents when she's overexcited or confused. I think we'll take some of your advice and just kind of wing it for those shorter periods we need to leave the house, but I need to be careful about routine. Both dogs are sensitive to changes. They get easily confused, and when they get confused they get agitated.

Since I last posted, the bully puppy is back. Reintroductions went well. I have to say board-and-train did wonders for the puppy. She's a lot more manageable now. We can recall her off anything, even food: Just yesterday we had a trigger moment where the puppy went for the mix's food bowl. They both had their muzzles in the bowl and were going rigid. The puppy came right off at my recall, came straight to me, sat down, and got showered with treats and praise. That's setting us up for success, where I'm not constantly having to stay hypersensitive to triggers and having to be right on top of the dogs physically. As much excitement and overall busyness the kids create in the house, I don't have the attention to keep that up all the time. Now that I can call either dog off and defuse any situation right away, it's a huge relief for me.

One thing that'll take some more time is getting the mix used to her kennel run. It's about 3 by 8 foot with her safe house at one end, so it's not as if she's crated, but she's none too happy about the confinement ... I'm having to up the ante all the way to peanut butter just to get her in there. Another thing is the walk. They both need more time separately before I'll try walking them together again. When I tried that a couple of days ago, they got into competing so badly with each other they were practically vibrating with excitement. So much for a "pack walk."