Also, for jigs, you could secure your jig with bolts through the grate. If you want any sort of precision you'll want to cut down to standard sizes first, otherwise lining things up will be impossible.
It depends on the actual size of your project, but from what I'm imagining I'd cut a "frame" out which holds your standard-sized blank (which you'll have to precut), and bolt that frame to the bed. If you use your starting point at one of the hard corner stops then you would be able to locate them pretty easily.
Second idea I have is to include some scrap locating nubs/holes on the piece. So, assuming your standard size is a rectangle, you'd have a rectangle with an extra nub with a screw hole in two corners. Then you can bold/locate it on the bed that way with no need for a framing jig.
Trying to aim precisely via the red aiming diode won't get you the accuracy you're looking for, so that's why I'd recommend some sort of jig. Also, I'm not sure but the new software might have a "move to X/Y" functionality which would make lining things up easier.