I apologise it took me so long to respond. The message arrived at, like, 4 AM
I tried the instructions given and they seem to work, though I won't say "perfectly." When saved as an archive, source folders do indeed become saved in their proper folders structure. When loading the project in, however, everything is put into a folder after the name of the previous project, with all source folders now being regarded as regular folders. This, however, is very easily fixable because all I have to do is right-click on a folder and go Source -> Use as source folder. This transforms it into exactly what I want. And because folders structure is preserved, I know where everything is.
I'm sure there's some way to build a project straight out of another project, but I haven't been able to find it. Regardless, this gives me a good way to transfer projects between machines, and is how I will require my students to save their assignments. Funny that the simplest, most basic concepts of programming are so often the ones which elude me.
Thank you kindly for your help, everyone
Never mind! Solved!