The short answer is you can only list one school when signing up for your TalkingPoints account. But here are some further details:
Teachers signing up individually: The school you list will not have any effect on your usage of the app, so you can simply choose one of your schools to list. When creating classes, you can work around this by naming the classes based on the schools they are at.
Teachers from schools that are partnering with TalkingPoints: Your administrators will be able to list you at multiple schools but this will be something they will do, not something you can manually do yourself.