The PEST module also has an online help system that you can use.
Also in FEFLOW 5.3, the PEST module in FEFLOW is limited to flow parameters. For parameter estimation for solute transport properties, you can use PEST as a stand-alone software, calling FEFLOW by a system call. There is a basic description of the process on the FEFLOW 5.3 DVD in the /doc directory. If you do not have such a DVD, please contact the DHI-WASY support team (support@dhi-wasy.de) to send you the pdf file.