Tom...
the devil's in the detail..... no easy way out. First up, I "zero'd" the mitre slots in the cast top using an accurate square and engineer's ruler. Raise the blade fully and set the ruler square to the blade right next to (but not touching) a tooth at the front of the saw. Mark that tooth with a marker (you'll need it again in a minute). Measure the distance between the tooth and the edge of the mitre slot. Now rotate that tooth al the way to the back, flip your square around and repeat. Compare your two readings, slacken the screws that retain the top to the cabinet and adjust by half the difference of your readings. Repeat as many times as necessary till the readings are identical. Zeroing the aux. top is much the same, although a lot faster. I left generous clarence in the brackets that secure it to the cabinet that the whole rig sits in. With the cast top parallel with the blade (btw that thing with the tooth compensates for any run out in the blade) the mitre slots in the aux top in-line with the slots in the casting, setting the fence is a simple matter of measuring to a mitre slot. I know the offset between the slot and the edge of the tooth, I simply add that to the size I want the piece to end up, clamp the beam down on that dimension (it generally takes a couple of checks at each end to verify) and have at it.
Like I said, it's damn ugly... far from fast... but it's accurate. The additional top gives me up to 30" rip capacity to the right of the blade.