You can synchronize your EndNote library in both directions:
Sync your Desktop Library with EndNote Online
Please note that ONLY ONE Library can be synced with EndNote Online.
Before your start synchronizing your library, you need to
To Sync your EndNote Library
Recommendations and Notes
You may get this message "You are about to sync or share a library that is different than the last library you synced. This will merge libraries. Do you wish to proceed?" This means that EndNote Desktop and EndNote Online will not sync correctly and you need to rest the Sync.
Refer to the following guides for tips and troubleshooting: