You can rebind some of the buttons in the game, but the issue is that in the menus A and B are swapped, and this can not be rebound.
That might be handled automatically by the Gamepad API in SDL2, hence the game usage of the gamecontrollerdb file. You can create your own mapping and add it to the source of eduke32 before compiling, but it's kind of a long shot. See https://github.com/gabomdq/SDL_GameControllerDB, the Mapping Tools section.
@mahcneto im sorry. I read your post wrong. Mine uses mouse look. Go into options, control setup, mouse setup, set vertical aiming to yes. And in advanced setup in there i dont have a digital up, down, left, right set up