The correct way to set out would be to find the high point of the ceiling, and the low point of the floor. This is your actual room size (should you draw a level line around the room and measure to the highest and lowest point you'd acheive the same as physically levelling both and judging it, but you'll also have some measurements in your mind [i.e. the amount each falls out of level) to help with your set out) and you need to work out the setting out with those factors included, but also the other obsticles on each wall such as windows and the likes, and even furniture if you want to make those look like they were meant to go exactly in the middle of a grout joint, or middle of a tile, sort of thing.
Spend time setting out, and the key is, to know where every tile will sit before you actually get the adhesive out. You'll know each cut size, and you'll have made quite a few adjustments to ensure they're all as best they can be.
