Note: The sequence of panel assembly varies by model. Shown here's the the Cape Fear (http://jemwatercraft.com/proddetail.php?prod=CF
Start by stitching the bow together. Lay the 2 bottom panels on each other and drill both stitch holes at the same time.
Keep the stitch loose for now.
Stitch the stern.
Place a stitch about every 6" along the bottom seam and spread open.
Locate, mark and drill the stitch holes for the frame.
Stitch frame into place.
As your stitching, you want to maintain a consistent gap. Avoid "hard spots" in your seams where wood rubs on wood.
Maintain the gap by inserting spacers as required. Popsicle sticks found at any craft/hobby store...also inside popsicles...work well.
The butt blcok seams should align (when using JEM Watercraft plans).
Continue stitching in the sequence your plans call for until complete.