I've been one of those crazy HS kids twice before, and here are my 2 cents!

Based on my experiences, these tips are best applied to large groups,

but are good advice for any sized groups as well. (The first time I went, it was my HS marching band, choirs, and orechestras = a group of 500 kids!!! the second time it was just the band so it was around 200).
Make sure lots of time is alotted to roll calls (when departing the hotel and the parks) and that meeting times are made clear. Also be sure that these times coincide with park openings and closings.
Be sure to tell students when they should be ready "at the buses" and have a suggested time that they wake up at (or arrange for your rooms to get wake-up calls).

Anticipate crowds for breakfast at the hotel, and think about how this will affect operations in general while in the park... alert students to allow extra time to make it to check-ins if it really seems crowded.
Consider issues that might be brought up regarding FastPass. I am assuming that you guys might hold on to the tickets for the students out of concern for the tickets' safety, but you may want to think about letting students hold onto them out of consideration for them to have a good time despite the crowds. This may be a decision that you aren't even able to make, but it's something to think about none-the-less.
Lastly, always have a chaperone station in the park for students who get lost, hurt, sick, etc.
Hope this helps, and have a blast!