It is a good idea I agree to do a fresh OS install on your SSD> When you do the install do not have any of the mechanical drives fitted just the SSD. That way the OS does not put the boot record on odd places. Also do a Clear CMOS before you do the install. Makes life easier in the long run I found.
As to speed, well you will or should find your hard drives are more responsive using the native SATA ports, they will not suddenly become blindingly fast. Mech drives are not fast at all when compared to SSD.
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