Is there a way to change the default keys? There's nothing in options but the instructions suggest it can be done.

I guess you're talking about duke Nukem 3D, the control can not be reconfigured in-game, you have to go to the directory of the game, run "Launch Settings", then choose "controller Steup" and "setup kyboard".

Do not forget to save your changes with "Save and launch Duke Nukem 3d".

If you've installed using a older installer and there is no launch setup shortcut then just click on setup.exe and drag it onto any dosbox.exe you have installed.