1- Potty training, when and how to start
ASAP. Bunnies will usually choose a particular corner to "go" in, and use that spot as their toilet. Once that is established, put a litter box there, and put some of their poop, and maybe even pee soaked paper (or whatever is lining the cage) in there. That will help them learn to use the box. Once a litter box habbit seems to be established you can try moving the box and see if they follow it.
2- How to clean up poop
Rabbit droppings are (or should be) hard, dry and relatively odorless. For stray poops that end up outside the litter box, I just pick them up and toss them in the box. For a larger mess (or if you don't want to handle it) I use a whisk broom and dust pan. For the litter box itself, I just change the litter when it gets too messy.
3- We have aspen shavings in her cage.. Is that okay? is there something other then that that I should use?
I use litter made from recycled paper (Yesterdays News, or similar).
For bedding I use an old bathmat and carpet remnants (he's not a chewer).
After some training Zoom-zoom was allowed to be a free roaming house bunn, so he sleeps wherever he wants to now. At night he often sleeps in bed with me. During the day he usually sleeps on the old bathmat in the kitchen closet. It's usually quite warm here in the tropics, so I put a 1.5L frozen water bottle (inside a cotton tube sock) in the closet for him, and he'll lean against it when he gets hot. I do lock him in the kitchen when I leave the house, mainly so I don't have to worry about hitting him with the door, or him darting out the door when I come home (he's quite the bold explorer bunn).
4- Can I let her out of her cage to roam around supervised?
Absolutely! Out time is important for bunnies. They are very curious creatures that love to explore their surroundings. They have a fondness for chewing wires, so some bunny proofing is a good idea, even for supervised out time. They can also squeeze into very tiny spaces, like under furniture or behind appliances or the entertainment center, so some bunny proofing there is a good idea as well.
For bunny proofing a lot of people use wire cube (NIC) panels. But beware of the ones sold at Target, about half their panels have larger holes that a smaller bunn could squeeze through (or a larger bunn could get stuck in). I got mine from K-Mart, and they all have 1.5" holes.
Here's a barrier I made from NIC panels to keep the Zoomer out from under my computer desk. The side pieces are for support, so it's self standing.
You can also get "cage wire" by the roll from most hardware stores.
5- She likes to come out of her cage, but when i put her back in she squirms a bit is this normal?
Only have her food and water in the cage, so she'll have a reason to want to be there. An extra litter box outside is a good idea, though.
One trick you can use to get her back in the cage is to lure her with treats. If you get a treat bowl that makes some noise when you drop treats in (like stainless steel), that will become a "signal" to call her into the cage. The Zoomer loves Grape Nuts cereal, and that makes a nice pinging sound when I sprinkle a little into his SS bowl. I also get carrot horse chews from a local feed store, and those make a nice, loud clang when dropped into the bowl.
I originally used plastic bowls, then ceramic, and now stainless steel, but he learned the "treat sound" for each pretty quickly.
6- Should I put toys in her cage?
Sure. Why not?
7- How often should we handle her? So far it's been twice a day at least
That varies from bunn to bunn. Some like to be handled, others do not. I'd say handle them as much as you can while they are young, so they get used to it. And make it a positive experience with petting/grooming and a treat or two as a reward.
Zoom-zoom is quite moody when it comes to handling. He loves to be petted pretty much any time. But some days he wants nothing to do with being picked up and carried, and other days he's fine.
Aloha, Tim