We like to use the Repository for work in progress as it allows renaming files quite easily. Working files during revisions is a bit easier and the version-ing is nice when you have to roll back.
Beware, I had a few files become corrupt and trash the entire history. Backup your repository often, or do periodic saves to the file system.
While work in process is done in the Repository, we publish to the file system when ready to release. It is a good backup if there are Repository problems, allows controlled release of public revisions, and provides a way to share between users when there are server problems and we are just unable to connect to each others repository (usually on a Sunday).
A tip on using the Repository, DON'T roll back to a previous version as that is destructive. Instead open older versions read only until you find the version you want, then just Save As under the same name and the new version will be added to the top of the list. It is a lot safer than rolling back too far, and you have a history of the bad/undesired versions as well.
We also use Backup On Demand for our File system, and it gives us the same versioning that is part of the Repository. We can always go back and look at a previous file system save (when enough versions are included in the backups).
Purge your Repository history periodically to keep it running fast. Do a Snapshot, and then use my script (posted in the Binaries section) to purge a folder at a time automatically. One user quit doing snapshots because it took 2 hours to finish. I introduced him to Purge.
Also, Create another Repository called Backup or Offload, and when you retire a project, copy that folder to that Repository. That way when you need it again, you can restore it to the "Backup" repository and not to your working Repository and possibly overwrite something. That way you can also have SnapShots of reasonable size and by project or sets of project files.
We keep our Repositories in a folder called AlibreRepositories on our D: drive and off the C: system drive. That way we can restore our system or reinstall Alibre without effecting our data. It is a good practice to move your data off the C: partition and maybe even onto a separate disk as well.