By navigate you need to use the cd command (change directory).
For example on my PC is goes something like this:
cd c:\documents and settings\XXXX\my documents\my ebooks
When I've entered this my command prompt changes to:
c:\documents and settings\XXXX\my documents\my ebooks>
What I do is keep a window open showing my ebooks that I want to massage. At the top of the window will be the path so I don't have to try and remember it or write it down on a sticky note that I invariably misplace when I need it. And since all the files are right there in the window I can easily type them into the kindlefix.py script.