I usually do them afer painting - although every stinkin' time I swear the next time I'm going to do the body post holes first....just never happens.
For the larger holes, I use a stepped sheet metal drill. They work awesome, but they are quite pricey.
http://www.irwin.com/irwin/consumer/...rwinProd100146
Losi 8T 1.0, Savage Flux - XL style, LST XXL, Muggy, 3.3 E-Revo Conversion and sitting outside 425hp, 831 Tq Dodge Ram Turbo Diesel. It SMOKES