You will soon learn how and when to use your Jake Brake, and you will love it. I almost always have my Jake set on the higher braking setting. The Jake really shines when slowing down entering a limited speed zone or holding a speed on a downsloped highway without using or only intermittently using the footbrake.
One thing you might check on is your Jake/Allison programming. Our coach was programmed to shift automatically to 4th gear when the Jake activated. I had ours reprogrammed to not automatically change gears. It took only a couple times for our engine's RPMs to go from 1,500-1,600 RPMs to over 2,200-2,400 RPMs in about 1/2 second to scare me. I like the manual control of downshifting, not the automatic downshifting. I had ours reprogrammed to not automatically downshift at all, but you can get it reprogrammed to downshift automatically to 5th gear or 4th gear. We stopped at the Kenworth Truck Repair shop in Pasco, WA for reprogramming. It takes only a few minutes once the computer connection point is located, which on our coach was under the dash plate.