We just installed Boxifier on our Windows 2012 R2 server. Dropbox was installed and synced prior to install. Once we turned on Boxifier, and started Dropbox as a service, the DropBox tray icon disapears, which prevents us from configuring Dropbox as needed, seeing if everything is synced, etc.
Boxifier for Windows Server has a status tab in its interface which helps you see if everything is synced.
When Boxifier is running Dropbox as a service the Dropbox user interface is not available. However, here is a workaround for that configuring Dropbox as needed:
Stop Dropbox running as a service from Boxifier.
Start Dropbox manually and configure it
Close Dropbox
Run Dropbox as a service using Boxifier.
Moreover, when Dropbox is running as a service you should be able to see the green and blue status icons in Windows Explorer in order to get an idea of the sync status. The status tab in the Boxifier interface is also a good place to see if everything is synced.