Thanks for the question. We have two fillers that work for below waterline applications: Marine Premium Filler (p/n 46004/5/6 pint/quart/gallon) and Marine High Strength Filler (p/n 46012/13/14 pint/quart/gallon). Both are vinyl ester technology, so they are usable under the waterline. If you are skim coating, try the Marine Premium Filler. If you need more structural support, try the Marine High Strength Filler.
The first step is to ensure a clean surface. Proper surface prep will increase resistance to peeling from the aluminum. Clean with acetone, abrade, then clean again with acetone until completely clean. Apply filler after surfaces are completely clean and dry.
Work life is about 10-15 minutes, and the filler can be sanded after 30 minutes with an 80 grit abrasive. If you intend to prime/paint, use a bottom paint compatible with aluminum and ensure the primer is compatible with the paint (order paint and primer from the same vendor if you are not sure).