I use the touch-up brush after the gun is finished then put a couple of coats of finish over my touchup to lock the stain in place. I use leather dye mostly.
Others probably have a better way.
I mentioned staining glue earlier. I use a glue in bow making called unibond, similar to the old resorcinol. It comes with two different color hardeners, one light and one dark, I like the dark. This glue is bombproof and will hold together on a flexing bow limb.
I mixed up some unibond today to glue in a few shims in on a poorly shaped precarve, this is the dark.