The configuration file consists of two parts: search queries and options for PubCrawler. After entering PubCrawler Configurator and generating your queries, keep clicking on 'Submit' until you reach the 'Store/Show'-page. This will present the queries that you have generated so far and gives you three options to continue with:
The last button will bring you to a page where you can modify PubCrawler options first before getting your configuration file. Again you can deactivate the inclusion of explanatory text by clicking the according radio button.
At the end you will see your configuration file in your browser. When you save it onto your harddrive you should choose text format. However, PubCrawler version 0.96 or higher manages to read over any HTML tags.
The first time you are running PubCrawler with your new configuration file you should use the 'Check'-option to make sure everything is setup correctly.