Question on mb fan connection- ssd

I am doing my second new build this weekend I am putting a 2500 on a Giga z68xp-UD3 and I am putting it in a new coolermaster CM 690 II and it has 3 fans with modular power and small 3 prong square plugs. Do I hook these small plugs right to the MB or use the modulars power connectors. I read that if I want the MB to control fan speed than use the MB if not use the modulars. Am I correct or is there a perfered way you guys recommend. I will not be overclocking for now.

FYi the case has a switch on the top that I believe turns off the led but does not control the speed of the fans.

I did get a Coolermaster 212 for cooling just for future needs that is hooked up to the cpu fan.

The board has SYS fan, 1 Pwr Fan and Sys fan 2, is there a difference for the case fans to hook up to?

Sorry for the stupid questions but thats the only way to know.

Also I am going to put a ssd in and the board has a mSata connection and I assume use that and not the Sata 6gb connections, am I right and what is the difference. Better yet which one should I use.

Thanks for the help.

R