I prefer the 1600 DDR3, not so much for performance as it is only a couple of percent higher. I prefer it because I can run in synchronous mode. There is very little cost difference anyways. As to CL9, again Leaps-from-Shadows is correct that CL9 is very close to CL7 in performance. I use CL7 – but that is me.
Setting up the timings should be a piece of cake. Just go into Bios and select XMP (probably profile 1). Bios will read what is stored on the RAM chips and set everything accordingly. On older systems this was kind of hit or miss, but newer systems seem to have made it more bullet proof.