Actually, you may have done it the "correct" way. Whether or not the player played in the tournament in which you adjusted his points, those points should show up in the Stats due to the fact that they were adjusted. Usually, a player added to a tournament but who never buys-in is not included in Stats for that tournament, but if you adjust the player's points or cash, they will show up in Stats with the adjusted amounts. This was added to allow penalizing players who don't show up for tournaments, but as you can see has other uses as well. So, if the player has joined the league but has yet to play in a tournament, load up an already completed tournament (in that league) and add the player to the tournament (but don't buy them in). Then adjust his points accordingly. (Make sure you save the modified tournament!)
Do the adjusted points show up in the Points column on the Stats tab? If so, then it would seem your Overall Score formula may not be utilizing points to calculate its value.