Ideally yes, move the projector to the distance that generates the desired projected size, keeping the projector beam as centered as possible while having the front of the PPM parallel to the screen. That way you only have to take into account what is called vertical keystone correction (actually the PPM will take care of that automatically for you) of the tilt.
And lastly, yes, leave your autofocus on if the projector will be moved. If you install it (semi)permanently, you might want to consider turning it off to not lose any fine adjustments.
Also, read this thread: FAQ: Automatic Keystone Correction