Here are some examples of hull deck joints. This should help you to decide what would work for you if you can determine what you've got.
"C" is a 'shoebox' style, "D" is an outturned flange style.. etc. However your boat may be different from any of these.... The Irwin diagram shows the same aluminum rail you're thinking of... (but think bolts/washers/nuts instead of those little screws) I suspect this is similar to your hull/deck joint arrangement. I've found several A30 blogs touching on the subject..