Ok, after working with BC for a few weeks here is what I've settled on.
There is no way I'll ever keep all my routes in BC, I've got over 300 routes I've created in MS and "saved" to think I will accumulate that may "list" in BC and have to load them each time I start BC is absurd.
What I have now, I have a backup file (BaseCamp.backup) with nothing but my home waypoint in a list called "home", if I want to start from scratch and don't need any POIs. I also have a back file (BaseCamp with POIs.backup) with all my favorite POI lists for when I'm taking a longer trip and want look at POIs along the way. I user "restore" and select the backup of choice. Now a create a "list" with my routes for the trip and "export" (Save) the list to a .gpx file.
Its not a perfect world but it works and I don't wind up with growing list that if I delete one that includes a waypoint from another list it DELETES THE WAYPOINT completely.