Both holes on the sides of the cam need plugs. The lower holes are just for mounting the timing cover. For the upper holes, the one on the passenger side takes a special tapered plug. Take a look at this thread with pics. Paul Kane explains it well.
http://www.460ford.com/forum/showthread.php?t=139162&highlight=tapered+++plug
http://www.460ford.com/forum/showthread.php?t=139162&highlight=tapered+++plug