Is their a way to queue messages in a business operation to be processed later? I want to process messages over a certain size on a schedule, but let everything else process in real time. Is their a way to do this with one business operation or would I have to queue the large messages in a different business operation?
AFAIK there is no intelligence in operation's message queue other than First came - first served.
You need to build the logic yourself. Having separate operations for large and small messages / priorities is a good starting point. You can then use poolSize setting to play with priority of processing (bigger poolSize means "usually" larger throughput.)