I just did two frames today.
Use Frame Saver (which comes with good instructions) or Amsoil's HDMP (Heavy Duty Metal Protector) which is available at some auto parts stores. It's the same stuff as Frame Saver, but not marketed for bicycles and doesn't come with instructions.
Boeshield T9 may work similarly, but my sense is that it won't be as durable of an internal coating. But both concoctions work as chain lube (Boeshield for bikes, HDMP for motorcycles b/c it's much thicker when it dries and gets gummy) and they're probably pretty similar.
I paid $15 or $16 for a can of Weigel's Frame Saver at my LBS, so that price ain't bad.
You should strip the frame down (remove seatpost, bottom bracket, and even the fork - you treat the fork separately). I plug the top and bottom holes of the headtub with paper towels, and make sure you've got bolts in or tape covering water bottle mounting holes. Spray about 4 seconds' worth into the top tube from the seat-tube hole (use the thin red nozzle that sticks into the head of the aerosol can) and then plug the top of the seat tube with paper towels as well. Rotate the bike around for awhile at various angles so the stuff can spread around and coat the entire inside of the tube.
As for the tiny holes in the stays and fork-ends, you should cover them either before or directly after you've sprayed the stuff into the tubes. The factor here is that the aerosol carrier needs a way to get out of the tubing, leaving the important gooey stuff inside. So when you're spraying into the chainstays from the bottom bracket end, there's a large enough hole (the one that you're spraying into) for the aerosol carrier to float back out. However, when you're spraying into the seatstays, and sometimes the fork depending on design, you've only got tiny holes at each end, and you need to leave the other end from the one that you're spraying into uncovered so aerosol carrier can float out that hole. Right after you've finished spraying, then cover the tiny holes at both ends with wadded paper towels held on tightly by masking tape.