It does not matter if the gasket is on the inside or outside, they alwasy go on the flange side regardless if it is in or out of the water.
I have a very detailed Bulkhead Installation Tips sticky thread on this forum that should answer all your questions.
What size drilled holes and what is the outside diameter of the bulkheads? Are they snug in the holes with little to no side to side movement? Are you tightening only hand tight with maybe 1/8 to 1/4 additional turn. Are you sure the leak is from the gasket area and not from the inside? You aren't using teflon tape or sealants on the bulkhead shaft and nut are you? Are they installed clean and dry and are not supporting the weight of piping and fittings which would could cause unequal stress on them?