it depends on what type of usb ports your using. I bought a cheap usb wall plate from china off ebay. I popped the ports out of the place and cut the same size holes in the dash. The ports were held in with snap rings and then soldered the cable to the corresponding pins on the ports and it works great
i use the usb ports off the front of old computer towers--there are literally a million different designs for holding the ports to the front-- i have ones that the port gets screwed to the front mounting plate, ones that the pc board for the ports gets screwed down, and ones that snap in. if you could post a pic of the ones your working with we might be able to help you a little more with how it should be mounted.
also, you said that you wanted to put it in a cup holder-- make sure that there is no easy way for liquids to get spilled, and fall into the port.
i like to start the hole with a one size smaller drill bit, and then make the hole square with a jigsaw blade. it is slow, but is more precise.
Needle files work great for finishing up the hole. I have a square file with two opposing surfaces ground smooth and flat that gets more use that any of my files and rasps. It works perfect in those corners.