Won't go where I want her to!

How long do you leave this puppy alone?  Do you crate her while you are gone?  Is there someone who could let the puppy out of its crate while you are gone?

Since this is only my second day with the puppy, I haven't left her alone very long yet. She has only been left alone for at the most 20 minutes. She always waits to use the bathroom AFTER I leave the room to grab something to eat or take a bath. (Because of the fact that everytime she starts to go in front of me I pick her up and put her on the pad.) I'm afriad she's learning to just go when I'm not there instead of going on the pad.
Tommorrow when I go back to school she will be left alone for 5 hrs and the next day she will be left alone for 6 hrs. I can't leave her in the crate because it's too long of a time and because she won't be quiet. I live in a duplex so the neighbors (who aren't nice people so they can't come and let her out) will hear her. I don't expect her to not have an accident while I'm gone. It's just I want her to go to the bathroom on the pad at least a little bit so I can reinforce its the place to go. That way when she's left alone for 6 hrs in the future she can go to the bathroom by herself.

Okay, that's a tough one, but here's my suggestion.  I assume that you have carpet.  Am I right?  I am in the process of weening my puppy Winston OFF the puppy pads, because he's getting old enough to where I can begin crate training him.  (I am at work for 8 hours a day, and I wasn't going to expect him to hold it that long in a crate.)  Winston easily chose the pad over the wood floors or my tile floors because it's absorbent, but when you have carpet or a rug (which I did, and I had to roll up for a while) they would probably rather go on that since it's even more absorbant than the pad.
This will work on both of your problems at once.  Tonight while you're home, take the top off your crate so that the bottom is exposed.  Sit it wherever you're sitting and just throw tiny little treats in it, so that the puppy has to crawl in it a little to get them.  Throw toys in and make it a very very good experience.  After he's not so scared of the bottom, put the top back on.  At this point don't make him go in it at all.  Just throw a treat to the back.  A really really yummy treat.  Throw his favorite toy in there.  Right now just get him to work on being able to step in without fear.  Don't shut the door at all.  I would feed him his breakfast and dinner in the crate.  Just push it all the way to the back.  When he steps in, praise him and tell him the command that you would use for him to go in his crate.  I just used "in", but you could use "get in your crate" or whatever.  Say it and pet him for a bit while he eats, then try to shut the door half way through his meal.  Don't make him stay in there too long.  Try to let him out before he whines and give him praise.  Do this a LOT.  Now the trick is that he WILL whine for a bit when you begin to put him in, but you can't let him out when he's whining, because then he will learn that whining and barking works.  Is there a room further away from the neighbors side that you can put the crate when you actually have to leave him in there for a bit so they can't hear him?  You have to wait it out when they're whining and then praise them when their quiet, again give another treat.  Now, I had to squirt Romy (my older dog) with a water gun a couple of times and say HUSH, but if you can avoid using that tactic, then do, because you want them to have good experiences in the crate.
 
Once you've succesfully had your pup in the crate for an hour or so, then take her out and pick her up and carry her to your kitchen or bathroom - a room with a tile floor.  Make sure you have a puppy pad in there, and that you don't have any rugs down or anything. Keep her in the room with a baby gate or block it off somehow.  If you dont' have a babygate I suggest gettting one.  They are very useful when you have a pup.  She will probably go on the pad, because it's the only absorbant thing in the room.  Treat her and praise her, then.  Also, you really don't have to do this after taking her out of the crate.  You can just confine her in that room until she has to go.
 
I hope that helps, and maybe some other people will come along with some more suggestions.  Good luck!