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I have the bed cleats locked in mine for strapping down motorcycle. I think if you can buy the stowable loading ramp, it'll lock on there with a bracket.........etc.
There are a bunch of accessories, both Ford and aftermarket, that use the boxlink system. You can also use etrack attachments with them, which opens up a whole new level of uses.
if you bought it brand new, go see your dealer. It should have came with the cleats. Everything else is an accessory. The Cleats come from factory with the truck, or at least my 17 did.
It's always difficult loading cargo and having the right hook locations, or something is in the way, etc. We actually came up with a solution for that.. our mounting rail system hooks on your bed header, takes up little room, and everything is modular. Pictures below!
My XL didn't come with the brackets, or the mounting plates pre installed. It does however have the mounting holes for the brackets, which maybe what you are talking about. I would take a look at your sticker and see if they were to be included. If you have the mounting plates, I assume you were supposed to get the brackets.