First read your instructions front to back at least once before you start. The purpose of the pins is to hold the wood flat on the board and in line with the plan. check often as you assemble for straightness. pin holes in balsa cause very little weakening to a point.
many other methods of holding parts work well also. I saw in here recently were a level and wieghts are commonly used. such as on top of a spar asembly. I keep a few garage sale levels on my bench for just that purpose. sometimes I build against one such as when starting a wing I'll keep a level against the LE. A stop by your local steel yard or any metal fabricator ...trailer builder etc. can get you a small box of "scraps" good for wieghts and angles. if you tell the guys there what you want them for they may help you pick some helpful pieces. you may have to spend a little time fileing those pieces before they make it to the bench and maybe clean some rust or oil off first as well. but once you have them you'll always have them.

A truely flat work table is key. holow core doors with a 2' x 4' cieling tile is ideal. the tile is easy to pin to. and cover your plans with saran wrap befor pinning and gluing...beats sanding plans off of the plane later[:@] don't ask how I know!

look at some of the build along posts here they have tons of picture and examples