first of all... Notepad++ is the best.
I use the notepad++ verborse backup feature and my god i love it. It has alyways saved me whenever i feel i have uploaded the wrong file... Although, i work on 20+ sites everyday... it's really hard to recognize which backup file is associated with what FTP? (i know i use Filezilla and notepad++ can't really figure out what FTP i was using i Filezilla..) my recommendation is the improvement of NppFTP plugin and backups.
So, if i am using NppFTP along with backups... it should really create a folder named the FTP hostname probably and start backups for files associated in that particular directory.
morelikey, it should create more of a Virtual diectory locally?
I know i am asking for toomuch may be... But i am happy to provide more details if anyone interested.
Perhaps not too much, but most likely it is the maintainer of NppFTP which is going to do it.
Please post again in the Plugin Development forum for more answers. Contacting the author is something I would do as well.