I found out through experimenting that the A and B headers of each channel can NOT be separately controlled:
http://rog.asus.com/forum/showthread.php?54471-Small-bug-with-Fan-X-Pert-or-bad-headersSo you really only have 4 different fan speeds you can control:
1. CPU
2. CHA1
3. CHA2
4. CHA3
So even though you can plug in 2 x fans on each channel (or more with Y-cables), you can NOT control the speeds of the A and B channel separately. So yes, you cant really chose where fan 1 "B" is. YOu can only chose where the fan(s) connected to CHA1 are, CHA2 are, CHA 3 are. There is no way to differentiate between the A and B channel.
And yeah, my fan x-pert also shows a red "0" on the B channels I do not have a fan connected to (my A channels are all connected).
What I am still unclear about, and don't have time to experiment, is if the CPU_OPT plug behaves the same as the A/B of the CHA headers. I believe it does, in that you can NOT have 1 x type of fan connected to the CPU and a different type of fan connected to CPU_OPT. Fan x-pert will get confused and mess up.
I run a Corsair H80i and I do NOT plug in the pump RPM plug into any fan port for the reasons above. It will mess up whatever other type of fan is connected to the other channel. That plug is just for RPM monitoring anyway, the pump never slows down on the H80i or H100i, it runs at max RPM. So I just live without the monitoring of it now.
Fan X-pert works great once you treat the A/B header of each channel like they are the same plug, and don't hook different fans (or pumps) to them.
*CPU: Intel 10980XE @ 5.0 ghz (by Core usage) w/ EK monoblock
*Mobo: Asus Rampage VIE
*RAM: 64GB DDR4 3000 G.Skill TridentZ
*Graphics: Gigabite 3090 Waterforce
*Monitor: Dell Alienware AW3418DW @ 120hz
*Storage OS: Samsung SM970 Pro (2TB) Windows 10
*Storage Games Internal: 4TB 850 EVO RAID0
*Storage Extermal: 48TB Raid0 (External USB 3.1 Box)
*Case/PSU: Thermaltake V71 TG/RGB + 3 Rads (120mm, 360mm, 420mm) + Corsair AX1200i PSU