Spirit System

I'm using the classic receiver configuration with an Spektrum AR800 and
a Hobbywing Platinum V4 ESC. The primary power with throttle connects to the receiver.
I'm using both Aux ports on the Spirit Pro so can I connect the Secondary power from the ESC to Ch 0
on the Spirit or should I connect it to the receiver ?

You can use a free port on the receiver to balance the load for all cables.

But basically both options you have mentioned will work, but only when both BEC cables are together, load is balanced equally for each.
If it is helicopter size 550 or smaller, it rather does not matter.

If you can use hot glue for securing each connector, it will definitively work well.