The only area of concern would be the bootloader. You are installing linux on the second SATA drive, but to boot into it, you'll need to let the bootloader (grub most likely) be installed on the first drive. It will give you the option of booting into linux or windows, but if it isn't on the main drive, every boot will result in windows being loaded. The only way around that is either to install the bootloader onto a floppy or bootable CDRom, or use the BIOS to select which drive is booted from. Those are all pains-in-the-ass to me, so I'd just let the install place the bootloader on the start of the first drive.