I just put together and booted my new build (successfully ). After installing Windows 7 (64 bit), and installing all the drivers / anti virus I need. I noticed only 1 HDD was detected after installation.
I have a Samsung Spinpoint F3 500Gb (boot) and a F3 1Tb (storage), both 7200rpm SATA HDDs. In Windows 7, the HDD doesn't show up in the Computer devices, BUT it shows up in BIOS and also showed up during the Windows 7 installation (as a device to install W7 to).
My motherboard is an Asrock P55 Pro / USB3 with AMI bios.
Yes. Normally when the drives are new, they are unpartitioned and seen as unallocated space. I am not sure where you found that information from; Windows 7 should be able to read hard drives fine. Both drives I take it are presumably new so they should be unallocated. The Windows installer had read the drives correctly and installed your OS to your 500GB drive.
Hope this makes sense, please let me know if you are confused on anything!