I am hammering in the frets with a small wooden mallet I made out of some scrap wood. you can buy mallets for this from stew mac, but I find that they are a bit to heavy for wooden guitars. You can actually just use a heavy mettle spoon if you lack anything better to use (i have in the past).

You want to use a somewhat gentle touch when doing this to avoid bending the frets or denting the fretboard. Also in cases where you have a bound fretboard, you want to make extra certain that the frets are centers in the slot to avoid damaging the binding and finish. I am applying some glue to these before tapping them in to help make sure that they wont move even if someone really messes with them.

On a side note, on a Rainsong if you didn't center the frets perfectly it could shatter pieces of resin out out of the side of the neck.