There are a couple of ways you can do it.
The easiest way to do it is to just drill through and use carriage bolts. To me, this is very arcade authentic as I don't mind seeing carriage bolts on the cp (some don't like any hardware showing)
For mine though, there were elements of my artwork that I didn't wanna mess up with carriage bolts so I bought pac man joystick mounting plates.
http://www.twistedquarter.com/index.php?main_page=product_info&cPath=190_196&products_id=443&zenid=dlk3joaeh3mqa43q5u7knvr8o5and had my mechanic weld them in place. because of the step design in the plate, it also gave me a nice little pocket for having my dust washers under the cp which I prefer.
I also didn't want my ball tops to stick up too high so I put a small spacer between each stick and mounting plate.
I also have the little interface board for my spinner and my lighting controller board installed on the underside of my cp. Obviously I didn't want that hardware showing so I epoxied a small half inch thick aspen board on the underside of my cp (the whole underside is sprayed black so it looks clean) and screwed them to that (with spacers)
Just a side note, with a metal cp I was worried about extra noise so I bought rubber gasket material and made rubber gaskets to go between my buttons and the metal cp. I did the same for the joysticks. And I also hot glued the switches on the buttons to keep down rattling.