Ben suspects that it is something sinister, that they are secretly expressing admiration for Charles Manson, but the explanation is more innocent. They are fans of the TV game show The Match Game and "Charles" is a tribute to Charles Nelson Reilly. It's an old joke among all the kids, and a remnant of when they used to get along better and have more fun together.
"Time is a great teacher, but unfortunately it kills all its pupils."
I believe the marker statement (which occurs when they go to the key party) is a reference to Joan Allens suspicion that Kevin Kline will place a mark of some sort on his keys to alert Sigourney Weavers character to the which keys are his (they have the arguement just after they walk in the door).