hello shaz,
firstly i'd prefer you'd just call me aby.
now,
the reason i said that the transistor would'nt do to well was because you are operating at two different voltage levels ,consider that you are driving a motor of 12V through the same transistor as you are firing the base with the 5V logic coming from the controller there is every possibility of the development of "back-EMF" which you know will most certainly find it's way into the source (Lenz's law), now obviously a poorly designed transistor circuit would result in the overloading of the transistor and as a result would then gain entry into the controller (this is possible even if you have a diode coming from the controller),thus damaging every area in it ,now if you have an isolated system as i have mentioned earlier there would be no physical contact of the two voltages hence your controller circuit is safe from the oustide world. if you still have problems let me know.