I marked a centerline on the rear TD skin and clamped it to it's forward bulkhead at the mark, then did my best to align the rear at the mark. Next I strapped it down and did any necessary shifting to make sure it overlapped the side skins properly. Once I was happy with it, my helper crawled inside and back-drilled through the pre-drilled structure while I held a wooden block against the skins; we started at the top and worked down to the sides. When the skin was clecoed on, I used a 1/4" bar up against the clecos to mark the skin edge distance, which became my final skin trim line (and, yes, there was a bit of trimming to do).
The forward TD skin went on much later but was similar. I made some marks on the rear skin at the proper overlap distance, then made sure the top skin covered these marks when positioned; you can use the same technique for the side skins to ensure you have enough overlap. The roll bar must not be in place when you fit the forward TD skin, but you can mark the side rails so you know how far forward the skin has to go. Fit, drill, and mark the rear and side edges as above. Also mark the forward extent of the skin at the longeron. With the skin off the structure, draw a straight line between the last two marks and trim the other three edges (don't trim that last line).
The next problem is the rear window cutout. If you've already built the canopy frame with it's side skins then you can simply put it on the cabin and use the side skins to mark the height of the window cutout at the front. Then you mark forward of the baggage bulkhead (the holes you drilled will be your reference) leaving room for the roll bar structure at that bulkhead plus enough for the skin to overlap the canopy. I decided a little more overlap than the bare minimum was ok, so about 3". Now draw your curve between the aft mark and either the left or right forward mark. Rather than trying to draw to both sides, I did only one and then cut it out and along the centerline to the front. I then flipped the piece removed and used it to mark the other side (it's not too hard to reverse the curve in the aluminum to do this).
If you're not ready to do the final cutout yet (because you don't have the canopy side frames to measure with or whatever), then use the above procedure but with, say, a 7" height from the longerons and about 5" forward. This will at least let you put in the roll bar until you are ready for the final trim. This is what I did, except I didn't trim high enough at the front, which made it more difficult to make the final cut. Notice, too, from the picture below, that I didn't drill the skin forward of the baggage compartment; that made it easier to fit the canopy later.
