If GOG have patched it to the latest version it should have joypad support built in. If not, then I don't know if it's worth looking at patching it manually - http://www.wcnews.com/webmirrors/tech/download.html
Thanks, I tried to install the patch but no dice, I get a compatibility error. I guess I'll just mess around with pad mapper and see if that does it.
I've sorted it - it is patched to the latest version, but you need to select the joystick in the install.exe file. The easiest way to get to this without too much faffing around is to edit the dosboxcrusader.conf file in the install directory, and right at the bottom change crusader.exe to install.exe, then launch Crusader from the GOG shortcut. Then change the control method, then edit the .conf file back to crusader.exe.
I had to do it this way, as the install.exe doesn't seem to like running outside of DOSBox.