Fan xpert only controls cpu fans and 3 outa 6 fan headers. And those 3 get controlled together. Not individually like I had hoped

Sorry mate I am not much of a fan controller kind of person. Consider this a free bump and I hope someone who knows more about fans and fan controllers will post up.

Fan Xpert will control the cpu fan plus 3 chassis fans, so that's a total of 4. All of the fans can be managed to a degree from the bios.

Here is what I use. I have 8 fans plugged into a Swiftech 8 way splitter box for my main radiator. This runs pwm from the cpu fan header. The pump runs from the cpu_opt header. I have the chassis fan headers all occupied and the optional headers occupied set to duty mode. I use Fan Xpert to control everything that it is capable of, which means a total of 11 fans total. I use only pwm fans.

I tried speedfan but never could get it to work the way I wanted it to.

Are you using all pwm fans on the headers? That's the only type of fan I've found that you will be able to control. If not then that may be the issue here.