a few more thoughts: Your problem will disappear as soon as you hook up your control box to a computer running satellite prediction software and let the program do the job. I'm pretty sure you will do that , because it's a fast paced job to control azimuth, elevation, tx-frequency and rx-frequency by hand while noting your qso-partners callsign, locator, name and report. This is especially true for the ssb satellites and even more when you do cw. Not so much for the fm transponders.
Let's say , a satellite's AOS (Acquisition of signal - or is it arrival of signal?) is at 300° azimuth, LOS (loss of signal) will be at 120° azimuth. That would be an overhead pass. Your satellite prediction software will rotate to 300° azimuth and to 0° elevation. By the time the satellite rises above horizon, the software will rise your antenna in small steps to the calculated elevation up to 90°. Once reached , it will rotate azimuth by 180° and begin to lower elevation when the rotator has reached 120° azimuth. Never will elevation be greater than 90° (which isn't possible anyway, because when you go beyond 90°, you decrease elevation, not increase it)