Let me know if I'm wrong but here is how I understand your question:
When you install Windows 7 on a second HDD it is modifying the MBR on your primary HDD to reflect the new Windows installation. (or at least it is modifying boot.ini)
To prevent this, just disable the primary HDD in BIOS before installation. Then the installer will create a new MBR on the second HDD instead of modifying the primary one. Enable the primary HDD again and then use BIOS options to choose which disk to boot.
Similarly, if you can find a way to hide the first partition while installing to the second partition the installer should behave in the same way as with two disks.