Everyday is different and you have to find out whats turning the fish on. If your going to fish a rod in rod holder you really have to be drifting this in itself imparts action on the lure as does the rocking and movement of the boat. For most of my snapper/squire fishing i use jerk shads and though these have very little action in them selves it doesn't stop fish nailing them while they are floated on the drift with the rod in the rod holder. The reason i suspect the are whacked is because they are well presented bait look a like and on the drift they are on the move and thus the fish doesn't have a whole lot of time to think about if they are "real" or not and whack them to see. Thats not to say you shouldn't work you lures, though when snapper fishing i find most pick the plastic up on the drop thus i usually only use subtle lifts and drops. Next time your fishing on the drift try one rod in the rod holder and work the other. You may every now and then drop some more line out of the one in the rod holder to drop it back a bit too. This technique will work in areas like mud/river to the deeper areas around Moreton. Give it a go you might be surprised how often the one left alone goes off. Oh and don't use too heavy a jig head on the floater you don't want the plastic plowing along the bottom and snagging up all the time but rather just floating off the bottom and or occasionally touching it (really depending where the fish are in the water column)
Cheers Chris