Plug 1tb into first SATA port, mark it Active
using Diskpart from Windows 7 DVD Repair Conosle or Repair CD, or use free Partition Wizard bootable CD. Then mark Inactive
500gb plugged into Disk1. DISKPART At PC Startup Partition - Mark as Active (Method Two)
Set 1tb on DISK0 as first HD to boot in BIOS setup, after DVD/CD drive.
Boot the Windows 7 DVD Repair console or Repair CD to Startup Repair - Run 3 Separate Times
until Windows 7 starts on its own and is correctly marked System Active. You may have to unplug the 500mb HD if it interferes.