I am trying to do a simulation of my program in Simulink, but the video says the VEX controller is not compatible. If this is the case, how do we test our programs with a simulation?
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If I understand the question properly.

To use Simulink simulation you have to put simulation input and output blocks:

For variable input blocks (the analog sticks and the accelerometer control), you have to put a constant and a variable input block in front of the control.

For 1/0 input blocks (gamepad buttons,digital and analog inputs), you need to put a toggle block in front of the block, and a display after the motor/servo. (you might start to see a theme of display blocks for looking at things motors,servos and inputs/outputs).

another place to find out about this is at this link (you can also get there by scrolling down on the BEST homepage).

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As widerbestrobot mentioned, you can use the simulation input and output blocks from the Utilities library to simulate your Simulink model.

In regards to using the VEX controller during simulation, unfortunately it does not work. You can however, obtain a Logitech Gamepad or an XBOX 360 gamepad and connect that to your computer and use that along with the 'Gamepad Simulator' block during simulation. 

For more info, watch this video:

Hope this helps.

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Search for  'Logitech Gamepad F310'. 
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