Deerhunter, here's a general photo sequence of my Seafari scupper replacement. Probably an hour job minus watching epoxy dry...
If your planning on using bondo, I'd steer you away from it and toward epoxy. Much better sealing the old wood, much better adhesion and much stronger.
It's important to seal the rotting wood block that supports the scupper tubes - that's how/where the water enters the bilge
http://s261.photobucket.com/albums/i...pper%20Repair/