I used the Assembly Features/Holes with "Create Part Features" and "Create Synchronous Cuts, Holes, Revolved Cuts if possible" options checked. I placed the hole on the bottom and it worked fine, however, I don't know how to find and edit the hole. When I create holes in the part environment, the hole is shown in the pathfinder, but it's not shown in the assembly environment.
Did you create part features, assembly-driven features, or assembly features? With the last two you should have them listed at the top of the pathfinder just under reference planes. If it's the first you have to go to the part.