deem

Duplicate. "Sync between two USB Drives on Same PC": http://forum.bittorrent.com/topic/23820-sync-between-two-usb-drives-on-same-pc/

There's absolutely no reason to create subdirectories if you want to sync the whole drive. Period.

In your case, a tracker is needed and is used of course. Next, an answer to "how" may be well-known technology of "hole punching": http://en.wikipedia.org/wiki/UDP_hole_punching

This is easy. Make new user. Login. Run BTSync. You have 2 BTSyncs running in separate processes, now you can emulate syncing of 2 hosts. Just checked it worked very well on Windows 7.

@nils: Ok, BTSync for windows is 32-bit and the author said: "sync a windows directory". Make conclusions. The author can dance with other settings, but it won't help. Problem is solved. You can't sync so many files on 32-bit app.

From unofficial FAQ we know that "if you're monitoring/syncing 1 million files, you will need around 300-400 MB of free memory". BTSync is 32-bit, so, it can only use ~2 GB of RAM. Therefore, the maximum amount of files is limited to ~6 million.