I would write down hdd model numbers and serial numbers. If for nothing else if you go trying to install the os. Or trying to set the boot order in the bios and have 2 same drives- the only way you know 1 from the other is maybe the serial number will be showing beside the drives.
I set my boot order as opti drive first and then main os drive as second and maybe a floppy as 3rd if the mobo even has a fdd- most new mobos have no fdd and maybe no ide either- so. For some things and if your mobo has a fdd you might have to change the boot order so the fdd or maybe a usb drive boots first if say you need to run memtest 86 or something. I normally turn off boot from other devices- which would be usb etc or on all my mobos any way. And is better security that way also.
It will be best for you to try and boot from the windows disc. figure which drive is what and have only it plugged into the mobo- get the os installed- then plug in your other drive.
Windows can bug during install if more than 1 drive is plugged into the system- I seen it here last week. Windows put the os on 1 drive with 1 partition and put the system reserve on the guys other hdd. That is wrong and gave him fits trying to format his second drive for storage. He had to do it all over again and with just 1 drive installed- it was a ssd c: as a fact.. We was all trying to help him get his second drive formatted and made me look real stupid. Its cool tho.
I also leaned something- the system reserve and os partition should be on the same drive. SSD are different and it was a 75gig drive- I figured it put the reserve on the other drive on purpose or is normal for ssd or being a small drive. I was wrong. Some other folks told him right tho- I guess he got it all going- I have not seen him post back yet- or have not looked for the thread etc.
I would set the bios for ahci support. Then install the os. Read your mobo manual or post at its home sites forum start a thread and ask or read through the treads on how to enable ahci support on your or a alike mobo. Your drives will run at their fastest in ahci and if they are sata drives.