The only way to be sure you will make square, straight cuts when using your saw guide is to make sure that the fence and stop are attached in proper alignment. That means that the guiding edge of the fence (the edge that guides the circular saw) and the alignment edge of the stop (the edge that rests against the piece to be cut) are perfectly perpendicular with each other.
The best way to align these pieces is to clamp a framing square to your base, with one edge aligned perfectly with the factory edge. Then you can set the fence (on top) and stop (on bottom) alongside the other edge of the square before attaching them to the base.