You just have to shutdown your alfresco server, move the alf_data folder to the alternate location you choose, and modify the dir.root to the new location.
The alf_data is created in the folder from where you launch the alfresco.sh script. if you launched the script twice from two different locations, then you'll have two alf_data created on your disk. In this case, you can wipe your database, erase the alf_data folders, and begin to rebuild your repositories.
(search for "more that one root node" into the forum, you'll find some details about that)
Everything should work fine afterwards.
Laurent.