Layout the part, scribing lines to the accuracy desired.
Prick punch (a fine 30-50deg punch) the scribed intersections. Done correctly, you should be able to feel the intersecting lines with the point of the punch but use a magnifying glass to confirm. An optical center punch is another option here, but again confirm.
Drift the center mark as necessary until it is at the line intersection.
Enlarge the mark with a center punch.
Optionally, with a divider using the center punch mark as an anchor, scribe witness circles the same or slightly larger diameter than the desired hole.
Select a very small drill with a tip that fits properly in the center punch mark. Some people prefer to just make the center punch mark larger than the web of the pilot drill they intend to use.
Drill while allowing the work to float on the drillpress table such that the drill will align with the punch mark.
Select the next drill, which should have a web thickness smaller than the original hole or punch mark and have a diameter slightly larger than the web thickness of the final or, if necessary, intermediate drill.
The floating method relies on a moving work-piece and flexing drill to align with a center punch mark. Horizontal rigidity is bad. Do not clamp down the vice or fixture and use jobber length drills. When drilling large holes, remember drill safety and consider indexing instead.
The index method relies on rigidity. Clamp and lock everything down. Use stub-length drills where possible. Use spotting drills if you have them.
Mixing the two approaches, using stub-length drills when floating to center punch marks for example, will give less accurate results.
Layouts on work to be clamped down and indexed will help with error checking but a center punch mark will not, in itself, correctly line up the drilled hole. It's up to the operator to correctly index to the mark.
When using the floating method, if the initial hole has gone off center then you can drift it back a slight amount. Use a cold chisel to notch the far side, the side you want to move away from, and then drill the next size up drill available, possibly repeating several times. Witness circles help with this approach.
When using the index method, if the initial hole has gone off center then you can re-index and use an endmill or, if large enough, bore it back.
If holes in multiple parts are to align, then bolt, clamp, or even tack weld them together and drill all at the same time. Another option is to make a drill guide (jig) that is then clamped to each part in turn.
The tables on light-duty drillpresses will often flex down with drilling pressure, thus going out of square. For this reason, deep holes are best done on more rigid machines. If necessary on a light-duty drillpress, block the table up to reduce flex. Optionally, shim the work on the table to compensate for the expected flex for the drill pressure being used.
Tramming the table is also important on deep holes.
A poorly sharpened drill can drill oversized holes.
