Not sure what exactly you mean by "formatting the HD and keeping Win7", formatting deletes all files on that particular partition of the HDD.
To do a completely clean install of Windows 7, you need to have Installation media (DVD or USB), and the Windows key. You also need to backup all your files. Then the steps are:
1) Boot the PC from the installation media (preferably with only one HDD connected, the one you want the OS installed to)
2) Run through the installation.
I wouldn't do a "combination" of HDDs, I would keep them formatted as separate "simple" disks.
If your HDDs don't show up in Windows Explorer after partitioning/formatting, check "Disk Management" under: Control Panel > System and Security > Administrative Tools > Computer Management.
You should be able to see all your formatted and unformatted drives in there, and you can repartition/format them.
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