Hi,
Re item 1, what version of VinylStudio do you have please? This was fixed, for most devices, in V8.5 and later, but I imagine you already have that. It looks like you will have to drag tracks across manually in Explorer, sorry. I'll take another look to see why particular drives might not be recognised when I can.
And yes, you can tell VinylStudio that you want tracks saved in different formats placed in different folders. Do you have the popup 'speech bubbles' enabled? If you do, mousing over 'When saving tracks, name them as' in the Settings dialog should actually tell you what you want to know. If not, you can click on the 'More info' link that you see there to be taken to the relevant topic in the VinylStudio Help file.
The keyword you're looking for is [File Type]. Insert it, at the point where you want it, into the existing string and add a backslash after it so that it's treated as a folder name, perhaps something like this:
[File Type] \ [Album Artist] \ [Album Title] \ [Track Number] - [Track Artist] - [Track Title]
The Help file could be better organised concerning this feature. I'll look into it.