Middle school is a tough age range. There is such a huge variability in talent, maturity, desire, etc. This is especially true if your middle school track team is 7th, 8th, and 9th grade like mine was. I don't know why this was the case because middle school included 6th, 7th, and 8th grade and 9th was part of high school, but this seems like a common age breakdown for middle school track. Ninth grade seems to be the year when a lot of kids start to run varsity type times, so having 7th and 9th graders on the same team creates a bit of a challenge. My middle school team had 400 runners running everywhere between 52 flat and 80+, for example.
You'll probably want to split the team into groups based on ability and give them somewhat different workouts. You want everyone to be challenged, but not overly so. Your older guys who are starting to become serious about running will be frustrated if they're just playing games all the time and your younger guys will lose interest if they're being pushed too hard. Depending on the size of the team, I'd probably do two or three groups. I'd try to have them doing basically the same things so that it doesn't get too confusing, but scale back for the younger groups.
Basically, the goal is to create a program in which everyone is challenged, but no one is overwhelmed.
In general, concentrate on providing a solid foundation for the athletes to build on rather than trying to go for immediate results. For distance guys, do mostly (or all) aerobic type stuff. I'd do more threshold type stuff for track workouts. The older guys can probably do a little bit of quality speed stuff, but remember that your goal is to help these guys to be the best runners that they can be in the long run, not just to make them fast middle schoolers.
Will you have any assistants to help you out, or is it just you? If it's just you, I'd try to find some volunteers to help with the sprints and other events that you aren't as familiar with. If there's a college around, I'm sure that you can find some gym teachers in training who would love to have experience working with the track team on their resumes.