We have a kitty with kidney problems and have "recipe" for a spray to help remove the odor. It is a spray bottle filled with hydrogen peroxide, a little baking soda (few spoonfuls), and a squirt of hand soap, gently swirled together to dissolve - do not shake. Spray it on the area to totally saturate it, let completely dry over a few days (it will probably smell worse before it gets better), spray again, dry again, until there is no more smell when you get it wet. That will help you clean your subfloor so when you put your new carpet down cat isn't repeatedly drawn by the smell of the urine that was there before to pee again.

We had one room with vinyl tiles which were very thin (1/8 maybe?) and we still could feel a little step up under the carpet in that area - but not a big deal in the scheme of things. I would try to get my subfloor as consistently even as possible before you put the carpet and pad down if it is in a highly trafficked part of the room, otherwise, I wouldn't really worry about it.