RAID controller are not compatible with each other, so dont expect a SIL formatted array working on a nforce, for exemple.
So, I dont understand why you said different connector, they are all the same in term of signal and size. some might have outside shell but even if the controller support SATA2, your drive should be compatible too.
What you should do is go in the BIOS and check to disable RAID for the nvidia connector you want to use,(generaly sata1 et 2(or 0 and 1, but the first 2 in the list)) and disable the third party controller, the Sil, if I'm correct.
Once plugged, check if the BIOS recognize the disks, then go ahead and install windows.. without the need for F6 or any special tricks.
I have the gigabyte k8nf-9. nforce4 SATA RAID is enabled for the first 2 connectors and run an array of 2x160gigs in stripping mode. sata 3 and 4 each had their own HDD as single drive. IDE1 and IDE2 has each an optical device...
There is nothing complicated with SATA.. unless you dont know which connector do what or if the controller has native windows support. Usually, third party controller, as the Sil or Promise need drivers for either SATA and RAID because they are not part of the chipset, but rather use the PCI bus, the same that drive the sound card, or the onboard sound. That the reason they need drivers. SATA controller, such as those provided by the nforce3 or 4 are integrated to the chipset, and will be recognized with windows as other IDE controller because they are programmed to answer to common request from the OS. SATA is only the interface. The controller use the SATA interface tor read the data from the drive. SATA drive are IDE, but has a SATA interface. windows has a standard set of command for IDE controller and ask the controller. the controller use the SATA interface to ask the drive that report back to the controller, whom report back to windows.
With third party, since they use the PCI bus, windows need drivers to communicate to the controller, just like it needs drivers to communicate with other PCI device. once it knows how to talk to the controller, thanks to drivers, then windows will install and fonction just as good..or almost.
RAID is another story. Even nforce 3 or 4 need windows to load drivers in order to operate. because the controller use a different mode and do not answer to common OS request. The drivers will translate the request so that the controller will understand the request.
In RAID, 2 HDD looks like one. If windows ask the controller for something on the disk one, the controller wont know what that means because there is no such disk one, but an array of disk.. Then the driver will tell the controller to look at the array one and get the data asked. This is the reason why RAID need drivers to work. be it native or onboard.
So, be sure to disable RAID for the SATA connector and plug your drives... and have windows install without any need for drivers. It has worked here..