I suspect they saw him on video, with packages of the same type, then looked at cell phone records to see if they had a ping from a cell phone in that area at that time, and then triangulated one (or more) phones to see where it led them.
A motel near there is a good place to look.
That sounds plausible. They still started with the assumption he dropped the package off at the store that blew up, but that would be a logical place to start looking.