Les,
I recently had mine programmed. Unlike Gerald, I had mine set so that when the Jake comes on, the transmission remains in whatever gear it was in when the Jake came on - ie: all 6 gears are available. There is still braking in 6th gear and as the coach slows, the transmission downshifts for additional braking. If I need something greater, I just manually downshift as Gerald stated.
The reprogramming is a quick change to the Allison computer, takes about 15 minutes, and cost me a whopping $35.00. It would have been free had I been bright enough to have it done at Harrisburg last year, when my neighbor Marty had his done.