If you haven't already called or emailed CLC's tech support, you might consider doing so.  I haven't seen the SIS plans so I'm no expert.  If the manual says to add 1.5 inches for scarf joints, you need to add 1.5 inches to the joining edge of one piece of each set of panels (or 3/4" to each piece).  If you have to scarf three pieces together to get a hull panel, two pieces will be 1.5 inches longer (or four edges will be 3/4" longer).  For example, if you take two 8-ft-long ply panels and lay them on your floor end to end, you'll have two separate pieces of ply that together are 16-ft long.  Scarf the two panels together using a 1.5-inch scarf and you now have one piece of ply that is 15-ft and 10.5-inches long. 

     If you scarf whole sheets of ply to the overall length you need, you can lay the plans down and draw your panels without worrying about the scarf measurements, the scarfing has already been done.  This wastes a small bit of ply.  By nesting the panel parts on 8-ft-long pieces of ply there is less waste and less ply for you to buy.  But you have to account for the scarfs, the overlaps of panels, before you cut the scarfs on the end of panels.  Or your panels will be too short.  Be sure you KNOW how long the individual pieces should be before you cut them and be sure you KNOW how long the total panel lengths should be before you epoxy them.  If you aren't sure, touch base with CLC, they will help.

I would suggest scarfing the panels together before tracing the pieces, no need to calculate for the scarf or alignment.

If you scarf after you cut out the pieces you must add 1.5 inches to one piece before you cut it out, and set the alignment properly to get straight panels.