The aux water pump works in conjunction with main engine water pump, but mainly this is a convenience feature: It does two things: on all cars it regulates flow: at idle or when stopped in gear, with low engine RPM's, it keeps full circulation so the heat stays hot. When you gun the car away from a stop, it works with a monovalve so you don't get a sudden blast of hot heat. The other thing it does it runs the "rest" function. When the engine is off, it helps circulate still-hot coolant for up to 30 minutes so you can have heat even after the car is off.
If people have problems with this, they just bypass the unit and let the main water pump do its job. One thing to note, however, is when the engine starts to overheat this extra pump can help cool the coolant quickly.

__________________
________________________
2002 Mercedes-Benz E320 4Matic
1995 Mercedes-Benz E320 Wagon
2005 Land Rover LR3 V8 SE
1999 Audi A8 4.2L quattro