When I first knew that I was going to have to fill some holes, I bought a little kit of West System that comes in tear open packages. Once I removed a few items from my boat and saw the likely extent of the problem, I bit the bullet and bought a gallon West with the pump system ($140). Glad I did. Even for filling a small hole, one squirt of A, one of B, and throw out what I don't use. Material costs weren't that much compared to the time spent on my project.
I also bought some 2-part clear penetrating epoxy, maybe a quart total.
http://www.smithandcompany.org/CPES/ Every penetration into balsa got some of this before a putty fill. On deck fittings, I put duct tape over the underside hole and basically poured the penetrating epoxy in until it wouldn't take anymore. You have to stop after a minute because the solvents in it can make the tape release. This epoxy dries without an amine blush, so subsequent epoxy putty, like West and wood flour, will adhere. And then should the epoxy plug fail for some reason, the entire area surrounding the plug is protected by the penetrating epoxy.
The West "putty" was mixed to the consistency of honey and also poured into the hole with the underside taped. Most of my holes were small enough that I didn't need to worry about heat build up as the epoxy cured.
My tests with epoxy putty lead me to use microballoons and wood flour (3:1) as the best screw holding mixture. I tapped all the screw holes into the epoxy plugs, but in the tests without any tapping the microballoons in the mixture seemed to crush similar to wood rather than having the epoxy plug split.
For holes through a vertical surface, I used a little paint brush to get penetrating epoxy on the balsa. If you wipe it up quickly, it comes right off. Then I used a thicker than normal putty to stick to the upper surface.
I bought a package of 500 "continuous feed" table napkins at a restaurant supply house and have used almost half of them. Wipe up a dribble and throw the napkin in the garbage can. Don't try to use it again or you will end up walking on it, sitting on it, etc. This isn't the time to recycle. Do something "green" on another project as penance.
I also bought a couple hundred Popcycle sticks, a hundred disposable latex gloves, 20 disposable eye droppers, a package of red "kegger" plastic glasses, and I kyped some little hot sauce cups from Taco Time. Some of the best deals were at an artsy craftsy store. Not chasing down a mixing stick or finding a cup that can be used again saves a lot of screwing around.
Mark