Carry the gear onboard in a mesh bag or a soft bag at any rate so you can remove it in the order needed and then stow the bag out of the way.
There's nothing different about diving from a boat vs a shore or pool as far as setup of your gear goes. If it's a rough day you can set the gear up before you leave port, but that's about all I could say about it. Entries are different of course, as is the rolling motions. If you tend to get seasick stay towards the middle of the boat and look out towards the horizon.
Have fun, I think you're trying to make it more complex than it is. Don't sweat it.