I guess MFFS is out of the question if you're struggling with air cells.
Build an underwater cube of sand/gravel (A filler over the water might be useful here), then cover the sides + top in dirt/non gravity block. Mine out the sand (filler is useful here too)- so you're left with an underwater box of air. (make sure there at least 1 layer of water above your box)
When your done building, simply remove that box and Ta-da! Underwater base of awesomeness...
-Or wait until redpower, wall your area off then drain it with the pump, Then refill when you're done building.