ahh - this I learned the hard way... ,
1. mark your centre line and mark the positions of where you want the machine heads to be sticking up.
2. then measure either 10 or 15mm in from the edge (depending on how wide your overall headstock is)
3. using a simple drill guide (like this) drill a 3mm pilot hole through
4. using a similar drill guide drill a 10mm hole about half way through the head stock
5. flip it over and drill through the other side. this way the 10mm bit doesn't make shit of the timber as it tears through the other side.
A drill press would make steps 2-5 a lot easier. I would note I've never gotten this 100% accurate, but close enough you'd need to look closely to see one was off. I've widened the holes in some cases to let me position the machine head a little more in line.
"Making shit of " I've heard called "bursting", but that might be a chippie term rather than a carpenter term. Also I never deal with your fancy timbers, just ply etc, and "the painters will fix it".
You remind me, I did learn that one the hard way, when there was no painters to fix it and no time and the project manager had a severe dose of Dunning Kruger effect.
As did I, to be fair.