The Default CFE is fixed so that the boot HDD is on the SATA port 1 and the optical drive is port 3; while they may be numbered differently, looking from the top with the front to your left, the 2 ports closest to the rear of the computer are for the primary HDD (closest to the top) and the one just beneath is the optical drive -- mine is a BD for use with Linux. I am away on business without my MB in front of me, but that is the way I recall it.
While you can rewrite the pop-up menu in the CFE for choosing drives from which to boot, I would wait until you have a working install. Just seems easier that way.
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