are there certain waters that the two pole permit doesn't cover? or certain types of fish it doesn't cover. such as if i am on a dock with 2 poles, can i use one to cast out for catfish, trout, bass etc. and use the other to fish under the dock for crappie/bluegill/perch?
The only exception that we can think of is during ice-fishing...you can't double the number of lines you use while ice-fishing.
In other circumstances, as long as you are in control of both poles, there aren't limitations on where you can use two poles.