Can I do a Clean install on 1 drive of a 2 drive setup?

I have 2 internal drives, 1 a 300gb which is full, and a new 1tb empty.
I want to do a clean install and upgrade to Snow Leopard on drive 1.
So I've just cloned hard drive 1 onto drive 2, with the excellent CCC. So drive 2 is an exact bootable copy. Can someone please give me some advice on my next move...
Is it ok to remove internal drive 2 from the machine, so i don't accidentally erase this disk (i cannot risk any chance of losing my files) while I clean install drive 1 with an upgrade of Snow Leopard?
Can I then re-fit drive 2 and copy over my software, preferences and settings to drive 1? even though drive 2 will be 10.5.8 - Is this ok?
Will all it's contents be seen when I re-fit the drive? - or will there be an OS clash? As both drive's will contain an OS - Does the OS only run from the drive which is specified on start up?
Thanks everyone

Is it ok to remove internal drive 2 from the machine, so i don't accidentally erase this disk
Yes, but as long as you are reasonably careful to select the 1 TB drive for the Snow Leopard installation, it isn't necessary to do this. In fact, if the other drive is almost full, the installer may not let you choose it.
Can I then re-fit drive 2 and copy over my software, preferences and settings to drive 1?
If it is full, then you could not do this in the first place. In the second, some of the software installed with Snow Leopard won't be compatible with 10.5. IOW, don't do it.
Will all it's contents be seen when I re-fit the drive?
Yes. Each drive will appear separately. If you give them different names there will be no confusion about which is which.
or will there be an OS clash?
No.
Does the OS only run from the drive which is specified on start up?
Yes.

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