I just posted a new thread on how to do this. First post so I may have sent it to the wrong place. I have a semi about top with the manual latch on the windshields.
Disengage the top motor by pulling the lever with the cable on it. This is the motor in front.
Then remove the toneau cover linkage which is a black bar about 6 in long on a crank arm on the toneau motor above the arm with the cables. You have to remove the clips from both ends and remove the link. Otherwise it will mess with the latch arm.
All done! To open the top push the top up button to release. The latch. Open manually. The toneau will not latch with the top up but that's ok the top holds it down. To lower the top, just operate in manually and hit the top down button to latch the toneau.
Much easier than I expected. Have fun