My combination is a VTEC 90 and Hi-Thrust 9.9 (make sure you don't get the High Thurst 9.9 or your economy will suffer) (just kidding).
Anyway, both engines are electric start and power tilt/trim. I have a standard Honda twin throttle quadrant, but two small separate starter key pads. (The idiot lights on the keypads are a little different for the two engines.) It all fits next to the helm in the usual position. Both electric trim controls are on the left throttle, which is the main engine throttle lever. You just leave the right lever alone most of the time.
The steering cylinder is on the main engine and there's a quick disconnect rod that couples the kicker to it so they both steer together. You can tilt and start either engine from the helm. I normally run with the kicker up and the main down. I can have them both down also. If I were to run with the kicker down and raise the main, my steering angle would be somewhat limited. (If the power tilt fails on either engine, there's a release screw that will lower them, so I can't get trapped with the main up and not be able to steer.) Running with the kicker, leaving the main down makes it steer better. Big rudder back there.
There's a friction lock on the kicker steering so I could release the link bar and lock the kicker from turning, although I haven't needed to do that. Because of the hydraulic steering, a person could add a second steering station in the cockpit. It's done often on larger boats. I guess I could also just remove the steering link and clamp on a tiller gizmo to the kicker....
I think I'd be out of luck for running the throttle from the cockpit, though. I don't expect that to bother me. Maybe later?? (It would be pretty easy to have a remote switch in the cockpit to just kill the kicker if that's what you want for dealing with a fish or something. You could wire a switch in series with the little emergency kill switch on the console. It would be just like pulling the little lanyard on the kill switch. Click, dead engine. Or tie a long string to the lanyard.....)
At the moment, the only thing I'd like to add to my setup is a remote power tilt switch for the kicker back at the stern. The big engine has one built in, but to tilt the kicker I need to climb into the boat and use the control on the throttle lever. It's handy when you're rinsing the engines after hauling out.
By the way, I don't know if the other new engines do this, but on these two Hondas you don't run the engine while flushing. You just plug a garden hose into the engine and let water flow through for 10 minutes. Water flows out of several places and you have a Honda water fountain decorating your driveway for a while. They specifically tell you to NOT run the engines. You could also clamp on the earmuff gizmos if you did want to run them, but why?
The fuel injected main starts so quickly you can hardly hear it crank. The carbureted kicker has an auto-enrichment feature so you just crank it and it starts and runs itself, almost like a fuel injected engine, but you can hear it fluctuating a little bit as it warms itself up for a few moments. There's no tach or hour meter on the kicker. Yet.
The kicker will run the boat up to near hull speed. About 6.0 or so. A single from a twin setup would run it a bit faster, but not much. (Actually, with big seas or wind it might do better than the kicker, so there's an advantage, although the Hi-Thrust version pushes pretty hard at low speed, so I'm not too sure there's much difference.) If you assume that an engine would fail every 2000 hours let's guess, you'd average about 2000 hours before you dropped from main speed to kicker speed. With a twin setup, you'd average 1000 hours before you dropped speed ranges (two times the probability of an engine incident). That's assuming engine failures. In reality, there's bad fuel, log strikes, groundings, whatever. With a log strike or grounding, having the kicker stored "up" means it's protected from these disasters, so there's an advantage that way.
The kicker has a quick connect fuel fitting on the front, so you could have a small extra tank with different fuel on hand, as an option. A good choice for a kicker is one of the Hi-Thrust models, geared down for a larger prop and lower boat speed. You get more pushing force that way at low speeds, and a kicker is never going to make the boat go fast anyway, so there's no point having a prop and gear ratio made for pushing a little fishing skiff at speed.
This all makes sense to me, but I can understand that others have different preferences, too. So many considerations and speculations to mull over, eh?
I don't talk much, but I type a LOT. Any more questions, fire away....
Jeff