Well, it's not that simple. Your ECU has to have the PWM outputs setup properly. But, if you're using an output like the AC clutch, or the VTECs, you'll be fine.
Don't run a different controller, just make sure you use a relay. A different controller won't talk to the hondata, and it won't know what is really going on with the engine.
I don't understand this one, but I'll try to explain it. With the full throttle launch, there's a switch that triggers it. On my particular system it's the switch I installed under the clutch pedal. When that switch is open, the full throttle launch opens up, and drops the rev-limit, allowing me to open it up all the way, and it also leans the fuel out a bit, to compensate for the whole standing still thing.
Now, with boost control, you'll set it up on an output through a relay, and the boost solenoid will control your boost, when triggered by the s300. If you have the boost controled via temperature (which is the only smart way to do it.) and via gear, you'll only boost up to what it set it to while that condition is true.
IE: If you have it set to boost at 2PSI in 1st and 3psi in 2nd, as long as you're in 1st, it'll boost to 2psi. Keep in mind that it can only figure out what gear you're in when you're moving, so if you're launching, you'll need a seperate boost control for launch. If you're not moving, it naturally assumes you're in 5th. Bad math, and you'll need to account for this.
I hope I answered everything. Lemme know if I was unclear.