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Doesn't matter which battery you hook up to. There is no primary battery on a Super Duty.
It won't hurt it to have 2 relays in line, but it does add another thing to troubleshoot if you ever have problems. I would recommend using upfitter 3 or 4 as they are only rated for 15 amps, save upfitters 1 & 2 as they are rated for 30 amps and you could use them on stuff that doesn't have it's own relay.
Rezvani's Latest Post-Apocalyptic Monster Is a Ford F-150 Raptor Underneath
Slideshow: Called the Fortress, the 850-horsepower pickup combines Raptor underpinnings with military-inspired features, survival equipment, and a starting price of $285,000.