First of all...such posts belong to the cmpro board...
wow..what a weird storing method
Scan them separately in terms of having them just physically stored in 2 paths and you still want 1 scan to check them all? Then this is currently not doable without some indeep knowledge and modifying the datfile and either adding rebuildto flags or using set subfolders. Not worth the trouble if you ask me.
Another option would be (but that would require not-merged sets) to keep 2 profiles for the same mame data. In one you go to set information and setup a filter "Select Sets: %c=?*" to only enable clones and in the other one you setup the same filter plus the "logical not" to only enable parents.
A fully freely assignement of rompaths to filters is on my to do list but don't expect such a thing soon. For now you can assign systems (bios relations) and mechanical/non-mechanical....