First of all: The issues you encountered with corrupted uploads were all bugs in Knossos itself. Resuming uploads shoild work fine and write-protected files shouldn't cause issues either.
IIRC the case with the write-protected VPs happened at the same time Knossos corrupted all uploads for existing mods. AFAICT I managed to fix all of these (these bugs are one of the reasons I still consider Knossos to be in beta state).
To actually answer your question: You can create a second base folder. By switching your base folders in Knossos' settings, you can test your mods but as I pointed put earlier, this ideally shouldn't be necessary.
Mods only have package subfolders if you're authorized to change/upload them. I call this "dev mode". Whenever you install a mod, Knossos checks if you have write acceess and installs the mod in dev mode if you do. If you logout of your Nebula account (I'm actually not sure if this is possible right now), Knossos won't install your mod in dev mode but you also won't be able to upload it.
I should probably write some unit tests for the upload code to make sure that I catch these bugs before they end up in a release. That, however, requires time I currently don't have...
I want to eventually create a portable version of Knossos; that would make maintaining two installations on the same machine easier.