It's a problem in Moriches Bay around buoys 29 & 26 due to severe shoaling. If you have an inboard, you may not want to take the chance. At a minimum wait for high tide when traversing this area.
Unfortunately Tiana Bay east of the Ponquogue Bridge is tricky as well. There is a great channel just east of Shinne**** Inlet that you could run to from the canal across Shinne**** Bay, however if you take the ocean to Moriches Inlet, be advised that Moriches Inlet is a total mess- avoid wind against tide and low water.
Another trick to following the channel is "red-right-rising", meaning if the bouy numbers are increasing, keep red to your right. Because Moriches Inlet is not officially a navigatable inlet, you may be thrown off by the red-right-return rule. In all of these areas, it is critical to stay on a proper track as the channels are extremely narrow. If you have an outboard, life is much easier. Go slow when unsure, and never try to motor off a sandbar. Have other passenger stand in front of boat to lift up stern, etc. If you are afraid of drifting and grounding further, drop your anchor. In most of these places it is hard sand, so you can get out and push. When in the immediate vicinity of the inlets (within the bays), watch out for extremely strong currents if you exit the boat- you could be swept away. Obviously only consider existing the boat when grounded within the bay, in calm water.
-Bill