with box or drop box, I can copy files/directories to a specific folder and it will be synced, however, I want to sync various different folders on my file system, is this possible? if not, are their other services that would allow me to do that?
Although not officially supported, it is possible.
To do so, you need to create "links" from the folders you want to sync to the Box.net folder.
This Wiki page gives you the details for dropbox, most of which should also work with box.net.
Personally, I use the Link Shell Extension to manage links on Windows. Contrary to some beliefs, the NTFS filing system has supported hard and soft links (UNIX/Linux style) for quite some time.
To reiterate, you create a link in the box.net folder to the additional folder that you want to sync. When you look in the box.net folder, it looks like you have your other folder there as well but it is just a pointer to the other folder.
Note that many of the Dropbox utility applications for this task seem to create junctions rather than links. Junctions are a Microsoft specific form of folder link that predates (from a Windows perspective) the more standard soft or hard link seen on most POSIX compliant filing systems. From a user perspective there isn't much to choose between the types, AFAIK a junction is very similar to a hard-link. Note that deleting a hard-link deletes the original as well! This doesn't happen with soft-links which are generally preferable in my view.