I used a small plane, and skimmed down a roughly matching bevel on both panels, allowing them to meet at a more or less flush angle so they could play nicely with each other. If you take it too thin, you will rip through the panels if you stitch out near the edges. Meaning you'll have to stitch deeper. My highly scientific (not) analysis led me to decide to bevel the panels to half thickness, resulting in a panel thick knife edge at the bow and stern of the boat.

Start stitching loose, and work your way tighter. The most important thing is to get those lines fair and symetrical. So if the ends are slightly off, leave it. Don't create bulges in the panels attempting to get the ends lined up perfectly. This is especially true if you're working with a bilge panel that is not cut perfectly symetrical (it won't be), or adding panels as you build up. Get the basic shape correct, as in flowing (fair) and symetrical. Fillet the joints, cut the wires, and then simply trim the ends to a uniform and faired shape.

I did initially try pre-drilling all my holes. Turned out to be a waste. Invariably, they didn't line up right. As panels would ride up or down on one another, it would shift the holes. It also had me with inadequate numbers of holes in some areas. I finally ended up going with some holes pre-drilled to get things started, and then I simple poked holes as I went along.