Hi Shane.
Yes, Leave the equipment side of things blank. If the vessel does get into the game, V-STEP themselves will add in their own equipment, which is the standard stuff that you see now (e.g. Throttle, Steering, Bow Thrusters). Also, things such as Radar, GPS (Map) etc.
So, it's worth your while putting together "Areas" to put all this stuff, but, don't actually bother putting in all the equipment, unless you somehow "Group" it (Like Sketchup) so you can remove, if you decide to send off your model. Or, you could even leave it there, and let them know, that that is the place where the equipment you suggest should be placed.
OR, you could have two files (When you've finished), fill one with all the equipment, one without. So then, you have one for rendering/display purposes.
Just my suggestion there.
Jack.