I would take the blue hide out at the bottom. Maybe take the metal ladder out, swap it for tie holders or more interesting things to climb.
I would always use a different type of bedding for litter, I'm not sure if its available in America but I use Aubiose for the main substrate and Back 2 Nature for the litter trays.
It's very easy, put litter in the tray, shove it in a corner and add a pee rock. Put any poops you find around the cage in the litter tray.
It can take them a little while to realise it's a safe space to do their business.
Rats can be very dramatic! She probably isn't too bothered by you, just a bit unsure.
Try putting your hand in the cage, holding a treat. They have to work out how to open your hand to get the treat! This can be a great way to bond.
Possibly add a Perspex tray at the bottom, so they don't end up kicking substrate onto your floor. It also allows deeper substrate which is good for digging and playing in.
Do you scatter feed them?