Don’t tell anyone, but Evil High uses patterns to produce some sort of consistency to the stories told. It's your game, do what you want, but if you follow these rules you'll thank me later.
Super Team has to be involved.
Even if the players write their whole plan around tricking and evading the Super High Super Team, they are the heroes, and HAVE to be involved. Perhaps there’s a mole within the school? Perhaps one of the players let something slip? However you do it, don’t let your players own careful effort lead them to a boring game with no super interference.
Super Team is Stronger than AP Evil
Early in the campaign, the villains will generally meet the Super Team, and get into a scuffle. Fighting is what the Super High curriculum is all about, and the Super High Super Team has been training for years to fight villains. This is Super High's first chance to fight, and they are over-zealous. Generally, Super High should win the fight so badly that the players’ characters come to hate and fear the Super Team. The purpose of this is to demonstrate that the villains will not be able to defeat the forces of good in a straight-up fight. They will need to be very clever. And Evil.
Super High is Watching
After the first encounter, if Super High doesn’t factor strongly into the players’ evil plan, the GM can keep them in the wings. Use them as a constant threat, just waiting for the players to screw up. If the players succeed at some part of their evil plan, let them see the Super Team on the news, at the scene of the crime. Make sure your players know that the super High Super Team is out there, and wants to beat them up again.