I moved mine to a large dog kennel so the litter could be there. Be sure to put in a box with a blanket that is upside down to let her have a place to hide. I didn't even need the kennel last time, my male was alert and ready to go within an hour of bringing him home, so off he went, and is fine. My little female really surprised me, she wanted out badly after two hours in the kennel, I let her go after seeing she was alert and walking fine, she acted like nothing had happened! That was two years ago and she is still spunky and running around. I think the worst is catching them and bringing them in, I actually get sick to my stomach. Some of my females have taken a couple of days to get back to normal, even refusing food for that long. But everyone of them came through OK. Good luck!
When I have kept ferals in a trap overnight. I line the trap with puppy pee pads. I then place the trap on a large tarp. Some of the cats pee in it, but since it is such a short time it's not a big deal.
I elevated the humane trap with the sides on concrete blocks so if they defecate it will fall through the cage to the ground. That's what the clinic told me to do anyway. I am planning on putting the girl in a larger dog crate on Friday when I release the boy and have already set up a small carrier inside the crate with a litter box in there. The cats haven't really peed or pooped though so it's still very clean as they haven't had much to eat the past two days. I've left food for them should they get hungry but they aren't touching it. All in all though I think if you're just gonna keep the kitty for one day or night the blocks will do and the waste should fall out. I think they recommended wood blocks but I didn't have any on hand.