It’s very normal for a rabbit to be nervous in a new environment with unfamiliar giants (like yourself). Some rabbits take a few days to warm up to owners, some take several months; it’s all about their personality and past experiences. You can help alleviate her nerves by showing you’re a sign of food security (treats). It may also help to just sit within her view and go about doing your own things near her, without creating too much noise. It’s important you’re as much on “her level” as possible, so pop a squat on the floor. Facing her may intimidate her, so pivot slightly away so she can establish you won’t be trying to attack her.

For the urine stains, trying to clean the urine as quick as possible may help, but considering your rabbit’s nervousness, I figure she’s hesitant to have you approach the area she recently peed? I use a damp towel, followed by a dry towel to spot clean Wick if he accidentally steps or chills in his urine. If she’s afraid to let you approach, just make sure she has plenty of water so she can groom herself until she’s more comfortable.