Is there any way to set up library files in subfolders? Does it all need to be in that one folder?

I want to be able to segregate my work-related epubs of websites from my epub books, so that I can sync one but not the other. (All my epub books are freebies, so I don't want to use up my online storage sync space on them, plus I don't need to access the non-work stuff at work; I want to be able to access the sugarsync'd work stuff everything.)

I've tried adding a subfolder to the library, but then the library doesn't look there or save there.

Right now I'm manually clicking each file at the end of the day to send it to sugarsync, which is a pain.