The aux fan should come on when the A/C is on, at the low speed. If the engine gets hotter, the fan will speed up (it has 3 speeds on your MY).
The FSU has no control over the aux fan - it's strictly to control the HVAC blower.
Ed in San Jose '97 540i 6 speed aspensilber over aubergine leather. Build date 3/97. Golden Gate Chapter BMW CCA Nr 62319.