Hi Dennis,
I would think that the migration tool would handle the tag queries in MII properly, but I am not sure whether there needs to be any other intervention in the transition from UDS to PCo. I would think that all you really need is to make sure it configures correctly.
Are you using the migration tool to convert your 11.5 objects/projects to 12.2? You will most likely have to modify your file folder structures according to the tool's requirements.
Regards, Mike