"drive 0, drive 1"? You talking about the SATA ports?
Check and see which ports are SATA 3 6Gb/s ports. Try to use those ports before reverting to the SATA 2 ports. Prioritize SSDs over HDDs for the SATA 3 ports. In reality, any port should "work". Just setup your BIOS so that it knows which drive on which port to boot off of.
Both. There will be less stress on the power delivery, elongating the board's life, and allowing a safer and better overclocking experience as you won't as easily blow your VRMs due to having more power phases.(not saying the M5A97 R2.0 has easy-to-blow VRMs, just that the EVO 2.0 is better)