I've seen this mentioned before and would appreciate some clarification on how to do this. Is this something I should always do when installing/uninstalling/upgrading mods? How do I do it? I think it has something to do with entering an interior cell, but spelling out the process would hep tremendously. Thanks!

A clean save is always relative to the mod in question, what it means is to remove the mod from your load order load a save game, make a new save that does not have the mod in it at all, and then activate the new version of the mod.

It is not always necessary, but can be useful.

You should deactivate the mod first, save with it deactivated, THEN remove the mod or update it with a newer version from the Data folder. Activate the newer version of the mod, if updating, then you can load the game up with the new save. Use an new slot for the clean save. Don't reuse an old one.

Also, some other mods might have further requirements. For example, you may have to go to a single cell area, wait 3 full days, then you can start playing (IE MMM).

A good list of directions on how to clean save can be found on the SDR website by Saebel.