Since the OP is still in school I'd suggest to not worry about the Jakes. Unless the school is teaching it, learn that from your trainer after you get the CDL. The stale green light and the point of no return are a really big deal. Also, I tend to go about 5 mph under the posted speed when I'm in traffic light territory.
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It's been my experience that it depends on the truck. I always used to downshift with the Jake on but the truck I'm in now... Ain't happening, which sucks cause I still forget to turn it off occasionally between gears.