It depends on why you want the custom folder.
If it is for personal use, create it in your home directory (and thing of that as the windows equivalent of %userprofile%).
If you want shared folder (e.g. a music collection for all memeber of the family, all with their own accounts) then user /usr/local/.
If you want to share the folders between your VM and the host OS, then you have two choices:
- Create them in the VM (in /usr/local/my_secial_folder_name_here/) and share that with the rest of the network. (E.g. NFS, samba, ...)
- Or create them on the host OS and use the hypervisors option to share that folder with the VM.
All options will work. But the 'right' option really depends on your goal.