1. Virtumart Templates are top-level the same as j! Extensions and VirtueMart Extensions.
2. Yes, I have a hidden menu named Downloads as below:
Downloads (Alias: downloads)
jDownloads » All Categories » List All Categories (Default)
3. Each category folder have a single menu category as below: :
VirtueMart Extensions (Alias: virtuemart-extensions)
jDownloads » Single Category » Single Category
See attached photos!