All I can suggest is setting up a simple controller (preset value control) under the 5LT section and attach the PWM fan(s) to it.
You can simply play with the percentage % on this controller and change the minimums and maximums on the FAN setting itself under Fans tab of the 5LT. This is just to start with so that the fan remains at a manageable speed for now. You can later work out how you want to align it to a curve control something more complex.
Now I'm using this method for 2 x MCP35x pumps that are typically PWM pumps. Although I cabled the pumps up so that "Power Control" is utilised and not PWM, as I have allocated each PUMP to an individual PowerAjust 3 (with temp, flow etc). Works perfectly. I can vary the RPMS of each pump to a desired RPM by tweeking both the FAN section and the preset value control as mentioned before. I do this as I run two different types of loops 1 x parrallel (Graphics) and 1 x Series (CPU).
(I can hear Mandrix now LOL).
My 5LT manages all the fans. I dont use the PWM port on the LT5 for now unless I add more fans. I've tested a PWM Fan a it can easily be controlled as per my mentioned suggestion above.