Brake In A Box Questions

I'm no expert but this is what I think is going on. The toad has an automatic transmission. When you follow the instructions in the owners manual to put the Focus into recreational tow mode you hear what sounds like a clutch kick out somewhere around the transmission and the message center displays "transmission ready". Then you disconnect the negative on the battery. When you reconnect it the clutch sound happens again and when the key is turned on the message center reads "transmission in normal mode". I fear that if the negative is connected in any way while towing it will kick the transmission out of tow mode which will eventually ruin it. Given the costs of everything these days I'm going to follow Ford's instructions to the letter. It sounds like a brake in a box is safer than one that's wired in a little tighter. Tried the Invisibrake but it somehow back fed thru the system and somehow lit up the Focus even with the negative disconnected so I had the installer remove it and never towed the vehicle with it. Roadmaster said disconnect the positive instead and Ford said don't do that.