How do you boot up from a 2nd drive?

I will be installing a 2nd drive and doing a clean instal of 10.6. How do I boot up from this drive, and then how do I transfer the files, favopurites and email etc across?

You asked if it transferred every folder. I answered that Migration Assistant does not transfer the old System, only your User files. Every single User file.
Once you have finished transferring your User files, you can stop using the old system drive, or even remove it and set it aside on a shelf as a backup, or wait a week or two and and re-use it for something else.
Once you boot from a new System drive, / (the root directory) is located on the new Boot Drive,  and new /Users is created there, and everything is referenced from there. Move your User files over as well, and the old drive will not be referenced any more.

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