You should use an aperture of f8 (stopped down) during the setup and alignment of LensAlign with the camera. The greater DOF allows both the Rear Plate red ring and the Front Focus Plate to both be seen in reasonable focus, which makes aligning them easier and quicker.
Once setup is complete and before you begin testing and adjusting lenses, you should always return the lens to its lowest aperture (wide open).
*Note: On some lenses, typically f2 and wider, the overall sharpness of the lens when wide open might make it difficult to ascertain the focus plane of the test shot. If this is the case, you might try to stop the lens down 1/2 to a full stop (for example on an f1.4 lens try f1.8 or f2.0). This will improve the overall sharpness of the test shot and make it easier to determine the focus plane in the test image.*