Not sure what you mean...
I hit 'Esc' and choose 'Save' to make a save game, if I just want to make a save game at some point and then continue on with a patrol.
I hit 'Esc' and choose 'Save and Exit' if I'm mid-patrol but ready to stop playing, and that would be the save game I load whenever I come back and want to continue that patrol from where I left off. Once I've done 'Save and Exit' I can exit the career, exit the game, shut down the computer, whatever, no problem. That last save game lets me pick up right where I left off when I go back in to continue that career/patrol.
But I don't do any kind of saves when I'm submerged or within visual range of another ship, cuz I've heard that can cause problems when such a save game is loaded up again. This is how I end up playing sometimes for much longer than I'd anticipated, because I get into a sticky situation that I have to get out of before I will risk making a save game.