there are 3 floors in my house as well, and i actually have a pee pad on each floor for milu. i started doing that when i was training her, because i wanted her to have access to it no matter which floor we were on. now she seems to think that she is used to having that. even if i remove the pee pad, she will still go where the pee pad should be.
i don't think it's a big deal to have 3 pee pads in the house. but if you don't like having that many litter boxes, then you can slowly move the litter box to the location you want. (but it will also depend on your pup, milu has favorite locations for going #2, she likes to go on the top floor, because we are rarely there, so she doesn't want us to see her when she is going #2)
good luck!
