I drilled the holes through the deck into the metal tabs that i had welded on the frame. i figured it would look cleaner if the holes were aligned with the deck - rather than the frame.
To do this i started by clamping the frame to the table, and then clamping the deck to the frame. I used an 1/8" drill as a pilot. each time i drilled a hole i left the pilot drill in the hole to maintain the board alignment. This is a nice trick if you have extra drill bits lying around.
The other approach would be to swap bits out, drill to 3/8" clearance and drop a bolt in.