Im a complete newbie to texturing but how about seperating various parts of your polygon submarine, and do some handy planar-mapping.

To seperate a poly surface;
1) Select all vertices at the border of separation and do the split vertices action.
2) Then simply chose the poly submarine and chose "Separate", and then you have two surfaces, making it easier to map accuratly with designer details.

Planar mapping can be on auto, or be set for a certain axis direction.