If I were to keep the file for offense equipped while doing battles, only using the frugality one when needing to stock up on meds…is this possible?

Yes, it’s possible, any many people do it this way.

Can I save a frugality boosting .moar file just for when I’m in need of meds or items? Or do you have to keep them equipped for a certain amount of time or something?

No, don’t worry. You can collect .moar files and items you never use, nothing will happen to them.