See the following threads for more suggestions:
http://www.rovinfo.com/viewtopic.php?f=9&t=540http://www.rovinfo.com/viewtopic.php?f=4&t=516What do you have on the dash? I presume you will want GPS. It would be nice to have one receiver and not have to have seprate ones for each system - Boat, Smart Tether, Side Scan. Does the boat have a basic depth finder? Also, depending upon budget, some daylight viewable screens with inputs would be cool.
A dedicated place for a pole mount would be nice.
Storage of all the gear is probably something you're going to have to deal with every day, so I wouldn't skimp there on making things easy to access, and not a lot of empty boxes in the way while operating.
A diver below flag.
What do you plan to use for power? I presume it has two batteries, but you might want to add a separate one with inverter for the underwater gear.
Food and water for long days.
I'm sure there are a lot more things people will come up with here to help.
And of course, yellow VideoRay T-shirts for the crew (and a seat for me)... (Actually, yellow is not a good color to wear if you are in front of the monitor, since it creates a bright reflection - darker color shirts are better for pilots or operators.)
Good luck with your project!
Tom