I am using XPAdder rather than joy2key but I assume it works pretty much the same way. You simply have the program assign a keystroke to a particular direction of the joystick. I found that I needed to use such a utility with my frontend (GameEx) if I wanted to be able to use joytick+button presses simultaneously, such the the alpha paging feature of GameEx. If you are having problems with joy2key, give XPAdder a try. It has a nice graphical UI, support for multiple profiles, and many other useful features.
Dave