It sounds like you haven't set up the controls using the setup screen.

Go into OPTIONS / CONTROLS.
Now click on the Joystick-Axis boxes repeatedly to select the correct joystick control to make it control what you want it to control.
On the right of the boxes, click on REVERSE if the direction is backwards to what you like.
Then press OK to save the setup.

Be advised, that if you launch EECH without the Joystick plugged in, all the settings go back to the default and you have to set them up all over again. I find that feature pretty annoying myself.