Sofakng--
Yes, that bit about "OH, the T-nuts go in the TOP of the CP if you are bolting from the bottom!" is the vital bit of information my brain hadn't absorbed before laminating the top of my CP (all the while wondering "gee, I don't know, won't the T-nuts just pull out?"--lol).
So yes, you would drill holes all the way through, hammer the T-nuts into the TOP of the CP board, then laminate, whatever. You now have holes from the bottom that end in these nice metal T-nuts that won't pull through.
As for sizes, it doesn't much matter as long as the bolt heads will hold in your joysticks, I wouldn't think.
-->VPutz