I use the Wheeler Jig, It works great.
I do not remove my barrels. To use the Jig with the barrel on you will have to grind a little off the end of the rod that goes into the receiver, this is easiely done but go slow and measure, I can post a pic for you if you need, let me know.
I set the jig up in my table top drill press, with the barreled action.
You can start the holes with the standard bit, then switch to a botteming bit.
Basicly a bit with a flat tip, you can take a standard bit an grind the tip off.
Use cobalt bit's, Not high speed bits. The high speed bits are to soft and you stand a chance of braking a bit in the receiver.
Measure your depth and go slow.
I beleive the Lupy or Redfeild one peice bases are the best, No Mod required.