I can see there's still confusion. I'll try to break it down further.
On your OS X system, you have storage, likely called "Macintosh HD". You can save files on it.
On your SheepShaver system, you have storage, likely called MacOS9. You can save files on it.
When you run an Application, say, TextEdit.app, on your OS X system, you can open it up, create a new document, and save it anywhere on Macintosh HD -- likely in Macintosh HD/Users/jb/Documents.
When you run an Application, say, MacProject Pro, under SheepShaver, you can open it up, create a new document, and save it anywhere on MacOS9 -- say, a Documents folder on that drive at MacOS9:Documents. (: is used as the path separator under OS 9).
If you want to access that file under OS X for any reason, you can go to the Finder in SheepShaver (the OS 9 Finder) and drag the file from MacOS9:Documents to your Unix drive. This will copy the file.
If you wanted to use that file in the future, you would open the Unix drive, select the file, and drag it into MacOS9:Documents. Then you can double click the file, or go into MacProject Pro and use File->Open to open the file.
Now it's possible that when writing out to some filesystems, you might lose the resource fork of the MacProject file, rendering it unusable.
Apple used to use, from Mac OS 9 through OS X Sierra, a file storage system called HFS+. With OS X High Sierra, they switched to a new file storage system called APFS (Apple Filesystem). This tells the OS how to store files on the hard disk.
As far as I know, APFS knows how to save resource forks just like HFS+ did. However, SheepShaver may have taken shortcuts in how it does things. Personally, I haven't had any problems copying files with resource forks from the finder in OS 9 to the Unix drive; my files stay intact. But years ago I stopped trying to do this from within applications like MacProject Pro, as that often resulted in failed copies. This hasn't changed with OS X High Sierra.
When I say "this virtual disk" I'm talking about the disk *inside* SheepShaver -- NOT the Unix volume, but one of the other ones that shows up on the desktop.
Do not save files to the OS 9 desktop by the way, as those files just get written into a hidden "desktop" folder on the related drive. This makes things confusing, as both the OS 9 disk and the Unix disk have a desktop folder, and you won't be able to tell which place the files are actually stored in.
Woah! What is this? how could it even happen?
I'm not quite sure how what you said here relates to what I said.
So if the only reason you're copying the MacProject files to the Unix folder is to have a backup copy, just stop doing it: the entire disk image that the entire OS 9 installation is stored on, plus MacProject and all its files, is saved in one (or possibly 2) files on your computer already, and THESE get backed up by Time Machine every time their contents change, assuming you have Time Machine enabled. Time Machine then allows you to revert back to earlier versions of this file, or just restore a copy of the file to open it in OS X and pull out an old version of a file that has changed.
Think of it like Russian dolls:
You have one big Russian doll (your computer's hard drive).
Inside it is a smaller Russian doll (the disk image you're booting in SheepShaver)
Inside THAT is the files and applications you're working on in SheepShaver.
Both OS X and SheepShaver have the ability to pull the head off the largest doll, pull the head off the next doll, and look at the contents. Just don't do it to both at the same time.
SheepShaver ALSO has the ability to poke a hole through the middle Russian doll such that you can move files between the smallest Russian doll and the largest, assuming you use the right tool to do it and nothing goes wrong.