I retract manually. Rear jacks are retracted prior to hitching up. After hitching, I check the lockout on the hitch and retract the front gear enough to do a pull test, then the front jacks are retracted fully. Then I look at all of the jacks to make sure they're fully retracted.
When we're ready to go, I do another walk around and look at the jacks again before getting in the drivers seat. I also double check the lockout on the hitch again on the final walk around. Also the sewer cap and the TV antenna and rooftop dish.
The extra walk around takes less than a minute. It's just too easy to miss something.
I never use the auto retract feature. And I take a lot of care when cycling modes on the control panel to ensure I don't stop in auto retract mode by mistake. Auto retract seems to me to be an operator mistake waiting to happen, so I make a point of avoiding it altogether.