If she peed on the cushions you can wash the covers in the washing machine and spray the cushions down with something like urine gone (it really does work). I actually use something called Pawls which is a cheap alternative from the dollar store. It does discolor stuff though so don't use it on visible fabrics. I haven't had trouble with the Urine Gone discoloring stuff but it's really expensive. There's another pet enzyme cleaner from Walmart I've tried but I can't remember the name. It comes in a white bottle with a tip kind of like a dishwashing liquid bottle.
I also use Oddball pet spray afterward to spray stuff down. It's REALLY strongly scented and you don't need much so it's pretty economical. Some people don't like the smell of it though.
Also on non visible places (like the cushions, but not the covers) you can spray with a bleach solution.
I've actually put my cushions in the bathtub before and washed with laundry detergent but I don't suggest that since they take FOREVER to dry.
As of right now I have garbage bags over the cushions on my couch under the covers so if one of the animals has an accident it won't soak through and i can just wash the covers in my machine.
For upholstery that is marked do not clean with water (you need to look at the tag, it will have a letter that is the cleaning designation that tells you what you can use) you will need to get a cleaner that isn't water based and use that first, then use the enzyme based pet urine remover and test it in a non-visible spot to see if it discolors or not.