Here is a two part series on layout for holes using 3 different methods.
[video=youtube;t6evpRPPlrY]
http://youtu.be/t6evpRPPlrY [/video]
The guy has a ton of other videos, all very good.
The cliffs notes are.
1) Coat part with layout fluid
2) measure distance to holes with whatever instrument you have (steel ruler, calipers, height gauge, etc) and mark with a scriber
3a) If you are using a drill press center punch (tip, if your center punch is sharp enough, you can get it to run down the lines you made with the scriber. If you are gentle, you will feel pretty clearly the place where two lines cross, that's where you're holes should be)
4a) pilot drill with small (1/16") drill
5a) drill to size
6a) repeat for next hole
3b) If you are using a mill, center the spindle using a center finder or wiggler
4b) lock the table
5b) center drill/spot drill
6b) drill to size
7b) unlock table
8b) adjust dials to needed offset
9b) repeat steps 4-6 for next hole.