TuneECU and PCV+AT are two very different beasties and won't conflict. The PCV+AT intercepts the signal after it leaves the ECU, does witchcraft to it, and then sends it to the injectors. You will need a map for it. Hanso has a couple of very good maps which he developed on a base tune from my bike (done by PowerTripp on the dyno) and from a map supplied to him for the PCV from PowerTripp. These maps work exceedingly well.
TuneECU will allow you, or a competent dyno tuner, to alter the tune inside the ECU. In addition, it will enable you to diagnose problems, correct them, remove fault codes, balance the throttle bodies, reset the ISCV, and a myriad other things.
I use both PCV+AT and TuneECU. I also have TuneBoy, but can't remember the last time I used it. If you plan on changing the air filters or exhaust then PCV+AT will sort out the A/F mixture for you with whatever (reasonable) mods you make.