To have a limit switch at each travel end for each motor (ie 4 switches), the only way to connect them to the controller is by using the inputs on the encoder module.
The manual shows a way to use all 4 swiches to trigger the Emergency stop. This method works on all controllers but it has a few limitations explained in the manual.
Another method is the swich and diode circuit that is also shown in the manual. The benefit of this method is that it works idependently of the controller, and is therefore safer.