That's a good point about the different rails. I also believe the first rail is always the ATX. I think the second rail is all the molex connectors, and then any more would most likely be PCI-e connectors.
Also about the HDD's spinning up... you could also (if you have a fan controller) flip off your fans and then turn them back on, as they take about double the power to turn them on initially as it does to run them after they've started. You want to always make sure you have consistent power, because that is what separates a *decent* powersupply from a *great* powersupply.