Basically, the barrel comes dovetailed on the bottom for underlugs, which you fit into the dovetail, just like the sights. Once the underlugs are fitted and tight, you gouge out a mortice in the bottom of the barrel channel for each underlug to slide down into.
Once you have the barrel sitting properly in the barrel channel with the underlugs down into their mortices, you're ready to measure, measure again, mark and drill the holes for the pins.
To do this, I pulled the barrel out and took my flat carpenter's square and put some masking tape on the face of it. I put the square on the top of the barrel, and made a line on the tape where the bottom of the barrel was, and noted which underlug that mark was for. (This is required with a swamped barrel, because the barrel is not the same thickness down the length of it. You could probably get away with a single mark for a straight barrel.)
Once you've measured two or three times and you're confident your marks on the masking tape are correct, you're ready to mark the stock and start drilling your holes. First, I used a Sharpie pen and drew a line around the barrel at the center of each underlug so I knew where to drill left to right. Then, put the barrel back in and transfer the line down the side of the stock for each lug. Then put your square back on top of the barrel, and make a cross-mark just below the line on the masking tape (about 1/16" below). This will put your pinhole just underneath the barrel.
Take your awl, and make a small indentation at your drill mark prior to drilling. This will keep the bit started where it's supposed to. Using your drill, have a friend/wife/whoever get down to eye level at the muzzle end of the rifle and eyeball the drill bit to make sure it's level on the up/down plane. You eyeball the drill from overhead to make sure it's level on the left/right plane.
Once you're confident everything is level, drill into the stock until the bit hits the underlug, then just drill enough to mark the underlug. Do this for all of the lugs, then pull the barrel out and drill the holes in the underlugs outside of the stock. This way, if your bit breaks while drilling the lug, you're not in a nightmare situation trying to figure out how to get pieces of broken drill bit out of your stock without ruining it. Once the holes are drilled, go back with a small countersink and put a very slight chamfer on both sides of the hole through the lug. This will help guide the pin through the hole when it's in the wood. I also like to work the bit back and forth and elongate the hole in the lug slightly to allow for a small amount of movement due to wood swell, etc.
Put the barrel back in the stock, push the bit back through the holes you drilled earlier, and just finish drilling through the opposite side. You're all done!