There was a suggestion a few days ago that to set your workpiece into a known location, fasten a board along the bottom and left of your work area and have the maslow cut a straight edge on those pieces (the cuts will be perfectly horizontal and vertical as far as the machine is concerned)
I just saw a youtube video from Mike Farrington that does this one better.
cut a 1/4" slot in your wasteboard and then you can insert some 1/4" plywood into the slot for your workpiece to register against, and when you cut the stop, you just insert another piece rather than having to cut the registration again.