Stock ecu needs to remain to drive the dash unit. I just got through installing a microtech with twiggy on another car (the owner of which I am sure is going to be talking it up on the forums once he gets the car back!).
Trick 1) resistor between the power and ground of the stock Air temp sensor...this essentially means that the stock ecu is still seeing an air temp signal (temp sensors are just temp sensitive resistors, change in resistance corelates to change in temp) - killing the battery warning light (f*cks me why it turns the bat light on, not the CEL....but ya get that).
Trick 2) this wasn't my trick, the dude who owns the car decided it'd be a smart move - install a second water temp sensor. There is probably a billion ways you can do this - but basically one for the stock water temp gauge/ecu, and 1 for the microtech. Result: stock ecu knows enough to make the instrument cluster water temp gauge to work, AND you get improved stock idle air control (because it uses this reading, along with other readings to work out what to do).
Trick 3) use the stock IAC. I use the microtech to control mine because i have to due to the way its all wired in. I don't recommend letting the microtech handle this job as it is really not designed to do it nicely....sure it works, but not well. The stock IAC, in conjuction with an auxillary water temp sensor will result in a way better idle, better cold start and hot starts etc and possible reduction in HOURS of tuning startup and idle.
Trick 4) Do as much as you can in the car. I used to think this was a bad idea, but the "brief" for the job I just did with twiggy was to make the thing cold swappable, something which we succeeded in doing by wiring 100% of everything INSIDE the car. Took a bit more working out, but the result was a more stock looking engine bay, and paradoxically better signals from the cam and crank sensors (probably because the splice occured away from things with high electrical interference like coil packs and so on.....
Beyond those tricks, you're on your own. There are other tricks for the australian version of the car relating to getting the tach working beautifully and so on - but we have different sensors and so forth.