Welcome aboard.
When you are in your office before going on a mission click on the sub on your desk. That will take you to the area where you can transfer or hire new crew, upgrade your sub or change your torpedo load out. There are a series of tabs once you are there that you can click to do different things. Check em out. Most of the interfaces are drag and drop. You can also promote crew and award medals here if it has been earned.
I believe this only becomes available once you start a carreer.
Also, by looking to the left in your office you will see an old radio on a shelf. That is the options menu which you need to set up in carreer mode as the main options menu settings do not transfer over.