The best advice I could give you is to get used to working in Windchill... always. You can still access your Workspace if working offline and you get the benefit of leveraging existing content (think nuts, bolts washers etc.). Plus when one of the what-if scenarios inevitably grows legs it will be much easier to make it "real" because it's already in Windchill and you won't need to spend (read waste) time resolving conflicts or creating duplicates.
You can pretty much do whatever in the Workspace and it's the Check In that pushes new or modified content into Windchill. You can Upload which will push content to the Server side of your Workspace and potentially get the benefit of backups, but without pushing your "what-if's" to the Server.
My recommendation would be to set your config.pro to map to Windchill located formats, start templates, custom symbols etc.
If you're dead set on working in Folders, then you can do a replace the format with Page Setup and navigate to the Windchill location for the "real" format. Much, much more to it when it comes to models so use caution and be methodical. I suspect that if you go through it once you'll recognize that it's easier to run your what-ifs in Workspace and back them up to disk if/as you need to store them.