I strongly suggest you add the syncing functionality for more than one library.
I had two libraries: one not important that I needed to share and one very important that I did not needed to share. Guess what, my libraries got corrupted, and I could only recover the unimportant shared library. I lost several important references through this process. Because you can only share your synced library, and that you can only sync one library, I had to sync the library that needed to be shared. Note that I did not wanted to share my other references by merging the two libraries (which would just be troublesome and destroy me attempts at organization).
Although I had a compressed backup of it, it was an old version just before the period in which I added most of the references. I know I should make very frequent backups, but nevertheless, the syncing function, if allowed for multiple libraries, would have saved me (and perhaps many other users) much unneeded trouble.
In consequence, I highly recommend that you give maximum priority to adding this feature for the next Endnote update.