In my opinion the seine net to protect the fatheads is alot more effort than its worth. Using dirt to dam up some small areas that can be flushed into the lake will produce much better results and tons of other forage like frogs, crayfish, etc etc as well as a crop of bluegills, shiners, fatheads, etc.
Also consider sprucing up the habitat like you briefly mentioned before, supplemental feeding bluegills to product more forage, or top down management with a few tiger muskies to do the LMB culling for you.