Syncing between your Desktop and Web libraries has several benefits.
EndNote Web provides a backup of your library data in case something happens to your computer.
Syncing your accounts allows you to access and modify your library while you're away from the computer that has EndNote Desktop installed. You can add, modify, and organize records in your EndNote Web account, and the changes will be reflected in your Desktop library the next time you sync.
You must sync your Web account to the Desktop software at least once in order to upgrade your account to the Premium version. This will give you unlimited storage space and access to more citation styles.