There was a recent thread where someone mentioned doing this.
IIRC the method is to rename the folder after the first install so that the second can't remove it. Edit the shortcut to point to the new name. The second install will overwrite the registry entries, so this should be the latest version, so you can play using the mods it produces. This means install old, rename then install new, so the old CS is available thru the modified shortcut, and the new one via vanilla.
I don't remember anything being discussed about how to separate the content location, so you don't make a mod unusable by editing it with the old version. Maybe you can't and it's a question of always re-editing with the new one to mark the esp as good to go.