Chad, I believe the thought behind repository groups vs directory server groups is to use one or the other. If you are going to use LFDS to manage users and groups then manage it all there. You would then go into the Admin Console for said repository and in the Laserfiche Directory Accounts you would add the LFDS groups for that repository.

If you want to manage users and groups from a repository level, you would usually assign the licenses to the LF Server license and do it all from the Admin Console. Obviously, if you go this route you lose LFDS authentication options with the web products.

In the end though, I find it is easier to decide where you will manage users and groups and just use that product to do it. I almost always use LFDS now.