I just brought a new cat into my home, we already have one cat. I set up 2 litter boxes because at first I was keeping the new cat in the bathroom while I was gone for the day. She will pee in the litter box but prefers my bedroom floor to poop. Grrrr. Any help will be appreciated.
My Thoughts:
Two main thoughts come to mind (assuming no medical issues exist, and assuming this was not a problem before coming to live with you). The first is general stress over a transition to a new home. Cats can take up to 6 months to become comfortable in a new house. Lots of reassurance can help.
The second is that it's extremely important to do the introductions properly. It's vital for cats that share space to work out their hierarchy, and either cat may feel threatened. If there's any tension (which you may or may not see) between the cats, unwanted behaviors can occur.
You need to work out any litter box problems with the new cat before introductions. If there are problems (with either cat), then you should go back to separating them. Is it possible you perhaps introduced the cats too soon?