In order to correctly trim your submarine, you need to use foam, both above and below the waterline. This closed-cell styrofoam board is perfect for this application.
 
The foam blocks can easily be cut with a sharp utility knife, scored and broken, sanded and installed almost anywhere in your model that there is room. Installation can be done with RTV silicone or two-sided tape. 
 
Foam is sold in blocks measuring approximately 2"x10", enough for most models of 3ft or less. For each additional foot of model, I would recommend another block be purchased. 
 
Product may differ slightly from picture, as the foam comes in pink or blue colors, and I'll ship what I have on-hand