Waxes are now being offered that can be applied to ski like a stick of deodorant. You can use base cleaners that you just spray on and wipe off. I like to iron on hot wax and then scrap it off before it dries. That really cleans the ski. Basically any damage that you think affects your performance you should bring in to be repaired.
Skis are just soft plastic, really, and so they can warp easily.
If your bases aren't perfectly flat then you can tune and tune and it won't make much difference.