Hi Hector,
I don't know if there is a simple manual... I think the only bottle neck is the interface which is not necessarily implemented in FEFLOW already ( not able to do unsaturated flow into PEST for example), but if you work only using ASCII file without the FEFLOW interface, you should be able to optimize any kind of model. You can download the PEST manual into the http://www.pesthomepage.org/Downloads.php.
Cheers,
Robin