One thing that is always a good thing to use are existing stories of hauntings and the like for the location you are using. Almost every place has its share of spooky stories, and they are an excellent way to get started. Also: any "supernatural incident at a college" movie could work as inspiration. Or maybe Buffy episodes, there is some great stuff in there.
You don't have to use supernatural forces to keep your players on their toes. If they need to get somewhere, local law enforcement or private security, or hell, just an eager RA might be enough to keep them busy. How about some student who suspects something spooky about one of the PCs and is trying to find out what is going on. Or another student in contest for an internship or a scholarship who gets in with the forces of darkness to have an edge over the PC he's competing with.
I often like to create "evil mirror" versions of the player characters to use against them, mostly in the form of lieutenants to the actual big bad. That way, each player can have his 15 minutes against his personal enemy, and I need a lot less time to prepare some generic threat. If you can establish them from the players background, that is even better. You can either do it in a 1:1 fashion, like focused practitioner against focused practitioner, or in an "unbreakable" fashion, making the opponent an opposite. The latter is more difficult, because you should still remain true to the character you are designing it for. For example you could send a werebear against a werewolf, strength against speed, something like that.
A good baseline should be the combined spent refresh of your player characters. If you spend an equal amount of refresh on the opposition in any given conflict, the fight should be tough, but winnable if the players work together. If you spend more, the fight is either going to be REALLY tough or not winnable without sacrifice. Knowing the bad guys weakness in advance should be the players objective before they get into a fight like that, and you should probably let them know that they won't be able to win this fight, if they try to push it (like someone else said: conceding is a good option here). Also NPCs don't necessarily take as many consequences as a PC, so that is an easy way to tone down the difficulty, if you realise you overdid it.