1. Place the manifold on the block and give it a little 'whack" to mark where the pins hit the intake, then take a drill a few steps bigger than the diameter of the pins and drill clearance holes in the intake, but be sure not to break through the other side... Just deep enough for the pins to fit and not hang the intake up...
2. Remove the pins in the block....
I prefer option #1 as I like the pins to be there to help hold the manifold cork end gaskets in place and help keep them from squeezing out and not leaking.... The pins help keep the gasket properly aligned, which may happen easier if you remove them...