I usually center punch my tang holes with a relatively robust center punch and a hammer. I know a lot of guys like the auto punches, but even the quality spring loaded punches will only make a light mark, so it's best to follow these up with a larger manual punch that you KNOW will grab your drill point. As long as your bits are sharp and the points are centered, you should be able to drill a fairly precise hole. Just make sure your table is trammed at exactly 90 degrees to your bit.
Once my holes are drilled into the tang, I usually just trace and cut two scales, then I put a drop of CA glue on each end and glue the two scales together. From there, it's just a matter of clamping the scale stack to the blade tang, and drilling through the holes I've already made in the steel, down into the pair of scales clamped underneath. The hardest part (which isn't hard) is just positioning the clamps where they won't be in the way of the bit or drill chuck. Sometimes I have to place a clamp on one end of the stack while I drill the hole(s) on the other end, then I'll clamp over where I've already drilled and remove the first clamp to reach any holes on THAT end. Hopefully that makes sense.... If I have too, I'll even just drill into the first scale about 1/8" wherever I'm gonna have a pin, then I'll remove the blade and clamps and finish drilling the holes all the way through the scales. After the holes are drill, just knock the scales apart and finish accordingly.
I've never had pins, corby rivets, or whatever, not line up when doing this. Just make sure the scales are clamped securely to the blade during the process of drilling (or marking) the holes.