So no, the snake won't be the same temp as the hot end, but I'm not familiar with what a snake's temp should be so I'll let more experienced keepers comment on that.
As far as what you're aiming at, the infrared temp guns only measure surface temp, so I would recommend spot checking throughout your enclosure, but pay special attention to the inside of your warm hide. I also like to check underneath my CHE just to make sure I don't have a hot spot on a branch or something that my snake can get to. Even though everything is controlled by thermostats, I still like to double check.