Will the settler I set up to a Supply Line belong to the town I send him from or the one I send him too? As far as counting toward max settlers?

They will belong to the town you sent them from....that is the town they start in.

So, heh, funny story...

The settler assigned to supply line MIGHT end up being the one you have to talk to for a mission (kidnapping, raider troubles, greenskins), and so you MIGHT have to chase that settler down between settlements to start or turn in a side quest.

Also, check your supply lines from time to time (L1 or R1, I think, on PS4, while in the world map) to make sure that your provisioners (settlers that are assigned to supply lines) are still doing their jobs. Had one disappear (died maybe?) between Warwick Homestead and Spectacle Island, leaving me without enough cloth to build more beds when the population jumped from 6 to 18, and had to find a new settler to assign to that route.