She probably peed because she was scared. Try picking her up facing away from you, scoop you hand in under her chest, and as you pull her up, curve (and support) her bottom away from you to face her from paws. This way if she pees again, it's away from you! This is also the easiest way to clean a messy bum
At this point, you can hold her close to your chest and clean the poop. Hold her reasonably snug, as shes not going to be too happy with what you're doing. But it's necessary and important that she doesn't have poop stuck to her.
The next question to ask is why is she always in her litterbox? Maybe the remaining area is not too comfortable? Change up the flooring/bedding on her sleeping area to see if you can make it more comfy for her. Or maybe buy a straw mat/box for her to sit in.