If you wish to target larger fish only then you should switch to larger bait.  Live Blue Crabs are excellent bait for large Permit, Tarpon, Snook and Jack Crevalle.  You will eliminate the pesky little Snappers from becoming bait thieves.
 
For the ultimate in big fish hunting in the flats try a large lively fish.  
Pinfish, Pilchards and Ballyhoo all make excellent bait.  I like to hook them once either through the lips or upper back.
 
They key to live bait fishing is the presentation that you use.  As I said before this sport is more like hunting that standard fishing.  When you locate a fish you need to gauge its movement pattern and present your offering accordingly.  To accurately present your bait you also need to keep aware of the current of the water and what it will do to your bait once it is cast in the water.  You do not want to cast your offering directly on top of the targeted fish, this will only spook the fish and result in a missed opportunity.  You should cast your bait in a manner that puts it in an area you expect the fish to move to.  Or you can also cast your bait so that the current of the water moves it towards the fish you have targeted.  By fishing in this manner you can keep you presentation natural and not spook the fish.
 
If you are an artificial bait specialist the flats offer opportunity there as well.  A weight forward jig retrieved through your target zone can work quite effectively.  I advise choosing jig with contrasting color between the head and body of the jig.

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