I Love My Cats — Please Help Me Understand Their Potty Habits

I'm not sure what I'm doing wrong or if this can ever be solved, but I need help in understanding their potty habits.

Lily, the younger cat (the one on top) has had an issue with the litter box since day one. She was a present to my Ashley on her 16 birthday and she has had a desire to pee on things that were on the floor since we brought her home.

Barley, the 'master' cat (not that I have to point that out, think you can tell by the look on his face) in the house and mine (we got them from the Humane Society the same day nearly four years ago, is more of a temper tantrum kind of guy. He is pretty good at doing the deed in the liter box unless he is frustrated at someone in the house.

I clean the litter boxes multiple times a week and completely dump it and clean the box with bleach once a week, but I don't always clean the boxes everyday. (that's hard to admit, but I have to be honest or you won't be able to help me) There are two boxes, one upstairs and one downstairs. I used to have both boxes downstairs as I read that they need to be convenient and Lily is handicapped. I soon felt that the second one, that I had put in the 'formal' living room/office was not really appropriate in proximately of the entryway. I then moved it upstairs. There is a cat tree up there that they both love and it is within 4 feet of that.

I have recently smelled urine in the 'formal' living room/office and am afraid that Lily might be going where the old liter box used to be. I have been more diligent about keeping both liter boxes clean, I sit on the couch so that they can sit on me and purr, I tell them they are beautiful and I feed them... what am I missing? Any advice would be greatly appreciated as I getting rid of one or both of them is just not an option.