I don't think it matters with the power plugs. If they put two connectors on one set of power wires, they intended it to be used that way. Internally to the power supply, I think they're all wired together to the same power rails anyway.

The fan RPM issue could be simply because the fan needs to have the extra "monitoring" wire that sends the RPM pulses back to the correct pin on the motherboard. If the fan doesn't have three wires, there's yer problem.

It's also possible that you plugged your case fan into the dedicated CPU-fan-only plug on the motherboard. That might tend to make the BIOS stop on you.

If your case fan is correctly plugged in and everything is working, there should be a BIOS setting that lets it ignore that fan's speed and boot without complaining.

You can also get adapters so that the fan runs from the power supply instead of the motherboard.