Ummm... Why did I just get a notification for this thread?
Anyway, about the brain thing: it depends on what you want to do. If you want to have an organism that either constantly sends a signal or oscillates use a neurocyte. If you want a left-right differentiation use a stereocyte (good for organisms that search for food and predators). If you want to float up because the walls kill you use a sensocyte. Of course there are many more things you can do.
So, about about signal input/output (you set all this in the signal's target cell, be it a buoycyte, stemocyte or anything that does something when zapped with the signal): IIRC it's the AxSIGNAL+B. 'A' multiplies your signal (if the sensocyte smells something its output signal get's multiplied by 'A'). 'SIGNAL' is whatever you set the signal value of the senso/stereo/neurocyte. 'B' is what happens when there's no signal. So if you set everything but 'B' to zero then it's just a regular dumb swimmer.
Sounds hard but it's not. You just have to play around with it. And remember to have the "brain" connected directly to the cell that receives the signal. It won't work unless you do some funky wireless signalling.