The way I do my flush setting is this:
Drill out the hole with a drill bit
Use a BUD burr, slightly smaller in diameter at it's fattest than
the stone to be set and open up the hole
Take the stone to be set and place it in the opening. The girdle of
the stone should sit or rest ever so slightly above or dip into the
opening a tad (you can always open up more but if you drill it to
large, forget it!
Use a HART burr at this time to cut your seat just below the surface
of the opening.
I use an old bur, snip off the top, file it smooth and polish it to
use as a "pusher"
Put the stone in place, use your "pusher" or whatever to set the
stone. If it does not go in, take the BUD bur and with your hand,
not the foredom, open up the hole, little by little until the stone
"snaps" into place.
This might take a number of practices to get the hang of it.
Hope this helps. E-mail me off line if you need further help