This is a bit of a guess. (I'm guessing you mount the separate partiton as a drive like an external drive?)
I have folders from External Drives and NAS drives added to PMS. I did it by mounting the drive in question and then whatever folder I wanted to include in PMS I dragged into a new Text Edit document that I had open (formatted as plain text not RTF - do that by SHIFT+CMD+T)
Doing that gave me the "url" for the folder on the drive, which looked like:
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In PMS in "Navigation/Share Settings" menu at the "Shared Folders" hit the green plus icon and paste the url from Text Edit in.
Then hit "Save" and "Restart Server"
I presume doing something similar with the partition in question should work?