Hi Andrew,
Boxifier does not remove the folder from its directory tree. You keep your folders in their original locations. Simply right-click the folder and choose “Boxifier - Sync with Dropbox”.
On a second computer the folder would be initially downloaded to the Dropbox -> Boxifier folder but you can then install Boxifier on that computer and relink the folder with a location outside of Dropbox (such as the one you mentioned from AppData).
More details on re-linking can be found here: Re-linking files from HD to Dropbox via Boxifier - #31 by mhauswald
