If walls and floors aren't exactly perpendicular, which side should I align tile with?
I think what you're saying is that the walls and the tub are not perpendicular and that you are going to tile the wall.

You want to know whether you should match a wall or the tub.

In situations like this my recommendation is usually to tile  in a diamond pattern or to use smaller or subway or mosaic tiles such that long, contiguous grout lines are not obvious.

However, if you are going to have long contiguous grout lines I would start by leveling them to the tub and the ceiling, possibly splitting the difference. Consider that a grout line that get slightly wider or narrower as it progresses is less obvious than a tile line that slants upwards or downwards dramatically.