WELCOME ABOARD!
All the major supermods (GWX, LSH3, NYGM and WAC) have varying amounts of ship-to-ship action, based for the most part on real battles, so if you read your history you can find them beforehand through hindsight.
No, you will not be asked to support them in these battles. As Alpha Von Burg said, your only real orders are to patrol your assigned grid. In the stock game you recieve a certain amount of renown (fame) for going to that grid, but it is easily offset by just sinking more ships at the place you choose to hunt at. That said, in the GWX supermod you will recieve convoy reports from AI u-boats, so there is sort of contact with friendly ships.
SH3 Commander is a tool which lets you adjust in-game functions with a single click. It also gives you a realistic career with your captain's background, and it adds names and cargo descriptions to the ships you sink, for a much more realistic feel to the experience.
Once you have the game and specific questions we will all be glad to pitch in and help you enjoy the life of a u-boat kaleun any way we can.