When I did the 1st aft side I set it on the supports and did the best I could for marking the inside chine but the 2x4's mounted on top of the hull do not let the side panel sit flush at the top edge and gave me a little grief after cutting it out, I had to shim the panel up about 1/2" to get a good fit.
I hope that made sense!
When I hung the second aft panel on other side I decided to hang the side panel from a screw mounted at the top of the panel at mid point into a brace and lined up the top of the panel with the chine, temporarily screwed the aft panel on then marked inside for cut. After marking and cutting I reinstalled the cantilever supports for the aft panel, the cut was perfect. Since this aft panel was marked and trimmed without the supports there was no tab to hold it at the perfect height like the forward panel. I could have reinstalled the aft panel, installed supports and shimmed for perfect fit but I did not, but was still very easy. I set the panel on the supports with the scarf joint lined up where I wanted it (after applying epoxy) and put the first screw in the top of the transom after lining up perfectly with rear chine ( just lifted up the rear) then lifted up the panel at the front scarf to line up with chine seam and put another screw in. On the supports the panel is stable, it sits out about 3" from the epoxy and rests against the chine and lifting it 3/4" is easy.
With 1-1/2" spacer under the cantilever support and the bottom panel trimmed + 3/4" I could have just set a scrap piece of 3/4" on the support and been fine that way. Those little scrap pieces of 1/2" I screwed to the support worked well, some out 6" and some close as needed for good fit and put some witness marks on made an easy install.
Tired and rambling on!
I applaud you and those who can write so someone else can understand / make sense of the worlds. I had to re-read/change my rambling probably 10 times and still.... question what the hell am I saying, haha.