WELCOME ABOARD!
All three of the mods you mentioned are great, and each offers a different experience. There is also WAC.
SH3 Commander is the perfect companion to any of them. It affects your career the same way as the supermods affect gameplay. You will have a more realistic crew loadout, the ability to adjust many in-game parameters with a single click, the ability to randomize events such as having your sub's skin change on a certain date, and every ship you sink will get a listing with its name, cargo, crew aboard and crew lost. It's the single most important tool for the game (at least in my opinion).
