I use EVGA Precision XOC mostly because I have an evga card and I use it to have my main cpu and gpu temp in the taskbar. And yes, I know other programs can do that as well, I've used afterburner, speedfan, HWMonitor etc.
If they are connected thru molex you cant control speed, but you can set it to 5 7 or 12V using jumpers, if you are using 3pin fan you should have in bios option or check if your mb has program for that