Disaster has brakes that are rubber pads on a lever/bar that lifts up to catch the bottom of the shuttles to apply the friction that stops them. The wheels for the shuttles are on the corners (obviously) and the brake pads are only about 6" wide, so they do not interfere. To get the shuttle to a brake, the track straightens out and the shuttle naturally falls to the center, thus can be caught by the brake - including the brakes and running rails at the end of the ride.
Remember, even though the shuttles are free to do what they want throughout the track, there really isn't going to be that much variation. If you look for old pictures of Avalanche Run (you can see one on my website under the "Disaster Transport" coaster page) you'll see streaks in the trough - that's where the wheels have worn off the paint. It really isn't that hard to get it to go to the right part of the trough for braking - the trough isn't that big.
'97 Disaster Crew
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PO!NT OF VIEW - A Different Look at Roller Coasters
http://www.crosswinds.net/~justmayntz/thrills/