Recently, my calculator's ram was cleared and I was working on a programs with several sub-programs running within it. I got the main control program back, but lost just about everything else. I was wondering if there is a setting to make backups for these too. If not, is there a way I can do this manually on the calculator?

I don't think there is a way to do it automatically (I have been in the exact same situation several times), but you can do it manually by going to all of your sub programs on the axe compile menu and pressing [Alpha], which will prompt you to confirm backing it up. (Doors will also let you edit archived programs directly)