eSATA ports on *-eSATA2 motherboards

[loophole]

This question is actually about the K8SLI-eSATA2 but I think it also applies to the whole eSATA2 range of motherboards (at least the 939SLI-eSATA2, 939SLI32-eSATA2 and AM2XLI-eSATA2 as they share the same ULi M1697 chipset).

I'm using the eSATA ports for the first time and my system has always had its SATA hard disk connected to the black port. I connected the SATA cable from the red SATA port to the red eSATA port to get the bottom eSATA port operational. And this works great, but the problem is that when I've got an eSATA disk connected, the OS now identifies the disk connected via eSATA as the first disk and so it can't find any partitions (because all the partitions that were on the first disk now appear on the second disk).

So my question to all you ASRock gurus is whether there is a way around this. I have a few ideas but I'm not sure if they're the right way to go:

The manual says that if you're going to use just one eSATA port then "it is recommended" to use the bottom one (which uses the red port). Why is this? Could I perhaps connect my primary hard disk to the red port and then connect up the orange port to the top eSATA port (making the eSATA disk the second hard disk)? Or will this cause some sort of weird behavior because the top port relies on the bottom port being connected?

Or, is it possible to use the blue and black ports for the eSATA, but if so why have the color coding the way it is and why stress the current cabling scheme so much in the manual - "Please make sure to correctly connect the SATAII and eSATAII connectors with corresponding color so that the eSATAII function will work successfully"?

Hopefully this will be helpful for others too.

Thanks!