To answer your question for yourself, you need to have a good understanding of the wiring and the way the isolator works. So here’s some additional clarification.
I created confusion by using the word “accessories” to mean user-added equipment like a winch, compressor, fridge, ham radio, etc. I didn’t mean accessories as used in the basic truck configuration. Sorry for the poor word selection.
I just did some measurements with my voltmeter and verified that the isolator relay is switched just as carkhz316 describes. The relay closes and connects the batteries when the ignition is turned on. The connection is via a 100 amp fuse and a wire that is smaller than a typical start battery cable.
Because it is contributing less than 100 amps due the length and gage of the inteconnect cable, I would not have described the aux battery as “used for starting.” Instead it is simply connected during starting because of the “non-smart” way they chose to control the relay. The ideal way to set up an aux battery isolator is to not connect the aux battery to the start battery and alternator until after cranking and after an initial two or three minute recovery period for the start battery. That would require more complexity and cost, though.
That less-than-100 amp current isn’t needed for starting (as evidenced by all the gas trucks with a single battery), but does help. You would not be able to start the engine via that wiring if the start battery was dead, though. If you want to have the ability to attempt a start from the aux battery, you would need a jumper cable arrangement or to swap the batteries.
You can connect your own user-added accessories to 1) the start battery (hot all the time), 2) to the ignition on bus via the fuse box, or 3) to the accessory bus via the fuse box.
With an aux battery, you have the fourth option of connecting your added accessory to the aux battery fuse block (hot all the time).
If you have the upfitter switches option, you could connect to those switches, which in turn are powered from whichever battery you choose, but the kit is set up for powering them from the start battery.
The advantage of powering your added accessory from the aux battery is that you can use it when the truck is not running, and even use it to the point where you significantly deplete the aux battery if you need to. The start battery will not power the added accessory when the truck is not running, preserving the charge of the start battery for starting. When the truck is running, you can continue to use the accessory and the alternator will recharge the aux battery.
Hopefully your options and the reasons to select a particular option are more clear now. Ask more questions if it’s still not clear.