It doesn't matter. SATA isn't like IDE where master and slave made a difference. With SATA every drive has it's own dedicated connection to the SATA controller.
I will say that you should install Windows first in a dual boot setup with Linux. It's possible to configure the Windows bootloader to boot Linux, but it's quite a bit more effort.
I have two hd dr`s on my machine my motheboard uses sata connections. I would like to know how to connect both drives which would be a duel boot system but I`m not sure how to go about doing that so I need some help. Can anyone give me the info that I`m looking for. I would be able to have both linux & windows. Thank you for your help in advance.