Hand controller gets disabled when I select auto functions

As a guess without further information, I assume your joystick has a connect/disconnect button which you have presumably configured as the button for “heading hold” (I’m assuming you mean “stabilize” or “depth hold”?).

That seems unrelated and should likely be in a separate topic. This comment on factors influencing the bottom lock may be relevant, but your issue could also be caused by damage or incorrect configuration of your DVL.