Oh, sorry... I just assumed we were talking IDE what with the Master/Slave thing (I always get a kinky thrill with that )
It's never a good idea to have two SATA drives plugged in while doing an install. IDE you're fine - SATA not so good.
Just go ahead an plug the SATA drive back in after the install - verify the boot order in the BIOS and migrate the files. If your system doesn't boot for some reason - unplug the drive and verify that the partition the OS is installed to is active. (reorder the boot order for the HDDs and reboot) If it isn't, you'll have to use the OLD drive to set the new drive to active and reinstall. I doubt this will happen. I've only ever seen it once and it was when I left all three SATA drives in while installing MCE.
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It's never a good idea to have two SATA drives plugged in while doing an install. IDE you're fine - SATA not so good.
Just go ahead an plug the SATA drive back in after the install - verify the boot order in the BIOS and migrate the files. If your system doesn't boot for some reason - unplug the drive and verify that the partition the OS is installed to is active. (reorder the boot order for the HDDs and reboot) If it isn't, you'll have to use the OLD drive to set the new drive to active and reinstall. I doubt this will happen. I've only ever seen it once and it was when I left all three SATA drives in while installing MCE.