It’s often wise to limit the space when the bunny is very young, but you really shouldn’t have fluff in the entire cage if you want her to be litter-trained, which is not so hard as it may seem + it’s a great advantage later on if you want to give her more space. She can have a diggy-box with torn-up newspaper + fluff so she can dig and have fun with it, but the cage can be fluff-free save for the litter-box. Fleece blankies (or pieces of) is often enough. In nature, wild bunnies never line their burrows with soft stuff except when they’re expecting babies; then the mum pulls her own fur out and makes bedding of it.
I think she will discover the awesomeness of the second floor of her cage sooner or later – most bunnies are a little cautious of new things at first and need time to adjust.
A play-pen is not the best choice if it’s fabric, fabric + bunny-teeth means the fabric will come out the loser every time. There are metal X-pens and other varieties of play pens that are better suited for bunnies.
I think 2 hs of play-time is rather a minimum for a young bunny, but that’s my personal opinion. I’m sure other members will offer more opinions and suggestions =)