Is she waking you up at night to take her outside to potty? Does she go when you take her out?
She is testing you and figuring out her limits, when she does go potty outside make a huge deal about it, prasie her basically throw a party, treats. This will help her to be eager to go potty and to please you.
Yes, you have to leave the box in the crate to make it smaller all the time. Until she is got the hang of things and is not using the bathroom in her crate.
Does she like treats? How are her eating habits? Are you putting down the food and she is eating it all within 5-10 minutes?