I too hauled my YJ on flat tow and then later on a tow dolly all over the place.
My config was auto in park and tcase in neutral per the Jeep instructions. In my case I had a 44 in the front and unlocked my hubs (detroit locker too)
I will throw this out here, you better make sure what you are flat towing WITH will not be pushed around by the YJ. My YJ had 35x12.5 tires on it and IT had MUCH more traction than the vehicle I was towing with.
The result was, I nearly jacknifed taking a slow right turn into Wal-Mart. I accelerated like mad to yank it back behind and never used flat tow again.
HOWEVER, and folks that has been around know what is coming. A year or so later, a young man bought my YJ, and flat towed it back to Florida behind his Ford Explorer.
A week after that, he was flat towing it down the interstate when someone cut him off in traffic and he had to swerve (going 60mph or so) That swerve caused his to lose control, ended up rolling and he was killed in the accident.
I found out a few month later when his dad called me, needing help on filing the insurance claims, etc.
When he bought the YJ from me, I told him in email and ph calls about how I nearly jacknifed and encouraged him to use a dolly. (I towed with dolly 5000 miles or so) Still I feel bad about this...so this is one of the ways I compensate, by telling this story everytime I see a flat tow thread pop up here.
Be careful...
Sam