Jay, your ammeter should fluctuate between positive and negative amps. Reading into your post, I assume you are telling us your system is not charging, and you are referring to the wiring at the voltage regulator connector. Yes, the individual wires within those pairs can be swapped, but doing so is pointless because the the two “generator” wires supply AC and the two white battery wires are jumped together in both the harness and inside the regulator.
If your system is not charging you need to measure the voltage at the regulator “C” terminal (referenced to ground.) you can measure this with the engine OFF and master switch ON. The C pin voltage be must equal battery voltage.