"what if I want to designate the site/location as Sales Reps name"

Open Lists menu > Other Names List. Put the Warehouse Name here. Now add this name as a Sales Rep. Now, use that field on your transactions.

"and sell out of their location when I received invoices from the field from them and also transfer inventory from the main warehouse to them."

Then you want them for Two Functions: One is Sales Rep and one is Site. The Program doesn't know this is your intent; you can do whatever you want to.