3 month female & 1 yr old male

Well for one thing, stop picking her up.  HE sees this as you taking his playmate away so he's not pleased.

They will sort things out for themselves.  If no one is being really HURT, as in blood and/or real yelping, nothing wrong with letting them figure it out on their own....as they would in the pack.  Also nothing wrong with saying "that'll do" when you've had enough.  But your PHYSICAL intervention is sending the wrong signals.

I would not allow an older dog to repeatedly body slam, or otherwise terrorize a small puppy.  Your puppy, at this point, needs to be protected from that, and needs to be socialized with puppies her own age, so she can learn canine language, and to stick up for herself a bit.  If she lets out one yelp, and he doesn't interrupt himself, it's bullying.

Whoa!  I missed the body slamming part.  Certainly if the older dog is being THAT rough. stop him.  But I still wouldn't be picking up the pup all the time.

Orion doesn't body slam himself on her. He weighs 15lbs. Bella weighs 4 lbs. Yes, that is a difference. My worrie is that he is too rough. I try to let them "work it out" but sometiems he pulls her by he ear and leg and she squeals. He will let go but at leats two times a night he will do this and she will repeativly squeal then I go out and pick her up. she hides under the table becasue Orion cant get her and plays with her toys.
 
Sometimes when I enter the room she will run and hide behind my legs. I know then she wants to be left anlone. I have thought about seprating then for a breif time, but I do ot want Orion to feel pushed out of the way or punshed. I know that it will take time for them to ajust to one another. She is 3 months and 2 days and he is 1 yr and 6days. She will get a toy and he will take it from her right away. Sometimes she will get up and go to get it back sometimes she does and sometimes she finds something else then he wants that one. I know he is trying to establish dominace. I am the alpha at home I want to make sure that Orion knows that I am still the alpha and that he is not the alpha over Bella.

Here's how to see if your smaller dog really wants to play with the bigger one.  Simply pull the bigger one away and watch what the smaller one does.  If she doesn't return to him, she doesn't like it.  They should be separated, or the bigger dog told to "leave it".  (Of course, you have to teach the "leave it" command first.)  I do agree with Glenda that you should not be picking up the smaller dog - it elevates her to a status she isn't entitled to in doggyspeak.

I used to just let my adults work it out with the pups.  But after my adults raised a couple of pups, I realized they were ending up with some of the same problems with interdog relations.  Two of my adults were instilling bad attitudes in the pups they were allowed to raise.  One is a very dominant female who aggresively would demand absolute submission from the pups - and she would hurt them, too.  Another, a male, hates puppies, just hates them, and would not accept any amount of appeasement behavior - so the puppies would never learn correct social behavior.

With the last three pups I carefully regulated all interaction with these two dogs.  The first one was raised by a wonderful old dog that was spending his last days with us.  The second, since I was more confident in my ability to read the two dogs that were bad with pups, I allowed limited interaction with them and simply interfered when it got nasty.  By the third pup, Maggie was much nicer and Ben accepted her immediately.

All three pups are confident with other dogs and my pack of six can all interact freely with each other - it's a great thing!