Moving to new from old (dead) MacPro-best way to xfer programs

I see two options-
Either boot from the new disk, and use Migration Assistant to move programs from my old boot HD installed in another bay. Will this work? Will Migration Assistant see the other internal MacPro HD's. And how do I assure that the MacPro will boot from my new boot disk, rather than trying to boot from the old one?
Second possibility-take out the new boot disk, and put my old MacPro boot disk (with up to date ML installed) in bay 1, and put the new MacPro boot disk in another bay. Will the MacPro preferentially boot from a boot image in bay 1 over the other bays? Then I and use Carbon Copy to make a clone of my old (slower/smaller) HD on the new bigger/faster one. Then install that in bay 1.
Will either (or both) of these techniques work? I would think the first is preferable if it will work since it will give me a clean OS install.
I am trying to avoid reinstalling my applications if possible...

Clone so you have a backup.
Use Migration Assistant.
A clean OS is ideal.
A new Mac can sometimes have an OS build that is later than that publiclly available.
As long as you keep a copy of the working system and leave it untouched, you are fine.
Move all the non system data off to another drive too.
Consider a Samsung 840 120 or 240GB SSD for the system.
No reinstall whether you use CCC or MA as long as they are compatible.
You realize you never mention the model of this new Mac Pro?
10..6.8 with its Rosetta works on any Mac Pro also.

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