Just checked the fans in my two S9´s and both exhaust fans are connected to the FAN5 connector. No problems at the moment with the fans ramping up and down.
I have one S9 and the fans do cycle up and down. They seem to be on a 13 second interval, and depending chip temperature, it either ramp up, down or stays the same.
Mine are currently cycling between 3 speeds:
Low: Fan3=3120, Fan6=4440
Medium: Fan3=3360, Fan6=4800
High: Fan3=4560, Fan6=6240
Typically it spends 2 cycles (26 seconds) in low, 1 cycle (13 seconds) in medium, and 2 cycles in high (26 seconds).
I have also noticed when I decrease the intake air temperature it decreases the speeds of the Low/Medium/High, most likely because the chip temperature is lower. Right now my intake air temperature is 24° Celsius, and the exhaust air temperature is 36° Celsius, and when the chip temperature exceeds 74° Celsius, it jumps to medium fan speed, and at or above 76° Celsius, it jumps to high fan speed.
As to what connector they are plugged in to, if I face the S9 from the air intake side (so the controller board is farthest away from me) then the power connector on the left (closest to the edge of the device) goes back to the air intake fan and the power connector on the right (closest to the middle of the board) goes to the air exhaust fan.