Put a strings on the high and low E positions (probably doesn't need to be strings though, string or cotton thread may be ok), and line it up that way.

Sounds like you need to sand the neck pocket a little too.Don't want it too snug.

To drill the holes line up your bit next to the neck and wrap some electrical tape at the point you want to drill to so you don't risk overdrilling and going in to the fretboard, or worse.

 

Yes, as LonePhantom said --

string up the outer 2 strings, position the neck, and be certain that the strings are equidistant from the edge of the fretboard and run evenly along their entire length (that is, you don't want the strings to run a little diagonal along their path, which would mean that the neck is canted to one side or the other). Also, be sure the neck is pushed solidly toward the bridge end of the neck pocket -- you want it very well seated there with no gaps. Use a little 220-grit sandpaper wrapped around a hard sanding block (chunk of wood) to remove a little wood from each side of the neck so that it's not too snug. You probably know this, but it's best to put the neck in from straight above the pocket -- don't slide it in from the headstock end of the pocket.

I usually use a hand-held drill bit to first mark the hole locations while the neck is securely held in place (stick it through the hole, push and twist by hand to leave an impression on the neck heel), then remove the neck and mark the proper depth on the bit before drilling (also as Phantom suggested). If the hole locations don't appear to be equidistant from the sides of the neck, best to check them again. A drill press is best to get the holes perfectly straight into the neck, or be very careful with the drill angle.