Quick SH3C ? (again lol)

Ok, I've read where you need to restart when running SH3C after each patrol so it can load the right files based on date, etc. Now, when I exit and go back in via SH3C, do I pick the save point that's in base after mission, or do I make what ever crew/equipment changes I want, load up, then exit and pick in base before mission? Or does it even matter?