Litter Box And Gi Issues

We got our 2 year old, Lily, this summer and have been dealing with some health issues since, mainly GI issues. Because of discomfort and soft stool, Lily started pooping outside of the litter box. After switching her diet and giving her flagyl and prednisone, we finally got her poop to look normal but she still wasn’t using the litter box for number 2. We just got her a third litter box that has lower sides. She proped herself on one of the sides
and she finally pooped in it! Only problem now is, we found pee that went over the edge. We now have a top entry litter box, one that has a hood but no door and this new one with lower sides. Anyone have any ideas on what to try next to keep everything in the litter box? Any suggestions welcomed. Thanks!

If she is propping herself on the side of the one litterbox to poop (and, then pee, I guess), it sounds like there is something about the litter box/litter composition she doesn't like?

What is happening with the other two boxes - the top entry and the hooded one?

My 12 yr old propped on the side of the box until he got arthritis and couldn't so switched to the floor. After trying every litter and other box fillers we got him to use puppy pads. He just doesn't like the litter under his feet. If all else fails put puppy pads under the box. Paper towels and enzyme cleaner in a spray bottle will make cleaning the outside of the box less of a headache.

She goes in all the litter boxes to pee so I don’t think the litter is the issue. I think it may be either due to still some discomfort with pooping or just how she started positioning herself when she was extremely uncomfortable. She has not gone in the other litter boxes to poop yet. We did just add potty pads under the litter box to hopefully catch when she misses. I just don’t want it to soak into the hardwood floors especially since we’re renting.

we used to put our large litter box on top of an extra large kennel tray, which was much better to clean than the floor. now we put a large piece of linoleum under the tray to extend further out - it's super easy to clean, and we didn't glue it to the floor, just taped it around the edges.