Does anyone know what to do when you have more than 99 engines on the Legacy Cab 2 system?
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You can't put more than 99 engines in it, so that's a moot point!
Get a second 990 base, and handheld, and set it to a different channel.
It is up to you to remember which handheld the engine you want to control is in.
NOT a good idea Paul, you can't have more than one base connected to your layout. If you connect, you won't have to worry about which base the engine is stored in as nothing will work! 
Gee John it works at the club, and at Trainfest in Milwaukee.
Remember, having command bases on different frequencies just affects the remote to base connection, the track signal is ALWAYS 455khz. Actually connecting the track signal of two command bases to the track will create havoc with the signals!
I can't imagine how multiple command bases connected at the same time can work, I sure have never seen it work. Just as a test, I connected my Legacy base and the BASE1L both to my test track, no joy, couldn't run with any reliability. It would occasionally recognize a command, but not consistently. That was also on four feet of track.
Are you sure you're not confusing connecting two bases with a serial cable and only one provides the track power?
