With cpanel i understand you can run multi boxes with IP clustering.

I am trying to understand how Direct Admin helps keep everything in order?

Or do you just run each box seperatly?

separately.
BTW. same regarding of cpanel. cpanel may use claster only for dns servers. also cpanel may use external mysql servers but honestly this is not cluster at all.
if you interesting in the control panel software with cluster feature (i don't speak there about load-balansing and failover on the fly features) you should look to hsphere (psoft.net) control panel.