When we have been they collected the fee at the entrance station and it was good for the entire time we were there or at least we were never charged again days later when we left. We stay in the park at the Watchman CG and always left the trailer behind when going out and about except when we left. In the busy months and hours they pretty much make the tunnel a one way road and the last vehicle through carries a baton to the other end and hands it off to a ranger on the far side who starts the process over again. At least that is how it has been for us every time we have been though it has been 4 years.