So for the relay boards, there is a max amount of commands I can send to the master board.  So how does one respect the entire command but allow for additional commands to be sent without their order being respected?

Create a double queue, the worst type of queue.  The first queue will break apart the command into usable chunks while the second queue will contain these multiple queues.

FYI, I'm being sarcastic about a double queue being the worst type of queue.  I can easily think of 20 other queues that could be worst, like the DMV, security line at the airport, being on support with Comcast or Charter cable ...