Wow a lot of new ppl are getting bunnies lately...and having trouble litter box training them!
If you read through some of the other threads on here, I'll bet you can find tons of advice for litter training rabbits, it's a common question. But I'll give you some basic advice
First of all, your bunny is still a baby. Babies are messy! You don't expect that human babies come home knowing how to use the bathroom, and you can't expect that of bunny babies either. As she gets older, she should start to develope cleaner habits.
Secoundly, I recommend that you get her spayed. That will really help her litter box habits, as well as prevent cancer, and problems she may develope in the future such as aggression and so forth.
How I litter trained my rabbits was I got them a nice big litter box, put yesterday's news on the bottom, then covered that with hay. Bunnies are strange, and like to eat while they do their buisness. Yes, they have accidents when they are young, but if you get her spayed and keep working with her, she should get it eventually.
About getting her back in her cage, what I do is I put something yummy in my bunnies cage, like their salad or a small piece of fruit, or you could even use pellets. Then I tell them it's time to go in their room, and they know that means that when they go back into their cage they're will be something tastey in there waiting for them and they can't get back into that cage fast enough. Of course, your rabbit won't understand this at first. The best thing to do is to put the food in the cage, and wait till she goes in there on her own, then say whatever command you want to use to make her go in her cage, and close her in. If your always chasing her around she could lose trust in you and that's not good.