Flooring Tile - Ceramic Tile - Tub Install

Okay, I actually have two questions here. I am going to lay 12"x12" ceramic tile in a basement bathroom (concrete slab in good condition).

First - while the slab is in pretty good shape, I laid out some of the tiles and can see that they don't sit perfectly flat in a couple areas (they can rock back and forth a little). I was wondering how flat is necessary, and if the thinset will or can help to make this work. It seems that a little thinker thinset in the lower spot would fix the problem, but maybe that's a bad idea.

Second - I went back and was reading some previous posts, and most talk about a tub being installed and then tile. I will be installing a whirlpool tub, and have been told by the plumbers to tile everything (including under where the tub will sit) and then they set the tub on the tile. Is this wrong, or can it work either way? Thank you very much for any help you can give me. Hoping to get this all done right.

1) So long as it isn't too bad, yes, the thinset will compensate to some extent.

2) I'd follow the plumber's instructions, but I've done it both ways and been fine.