You can't have it both ways. If both operating systems that you are booting can't see SATA then you can't use SATA without switching the bios emulation at start up each time. Linux has good support for SATA. It just has to be enabled in the kernel. I think most of the main stream distros are shipping with SATA enabled kernels now.
As far as filesystem set up, you can look this up on the internet. There are great resources out there for this. I'm not going to repeat them here.
You will have to set up the file system during the install to use SATA with raid and also configure the boot loader for raid accordingly. I know you didn't mention it but I'm assuming you're looking at raid because you mention HDDs, plural?
Otherwise it just needs to be enabled in the kernel for Linux.
Try this for starters even though it's a bit dated: