i believe duty is the amount of spike it allows to find the desired boost level, for example, if you want a boost pressure of 1.2 bar (does the apexi even read in bar i thought it was kg/cm3 or something, or is that the same as bar?) and you allowed a duty percentage of 25% then that would allow the apexi to spike up to 1.5 bar to find the 1.2 bar quicker, rather than a lower or 0% duty setting that would mean it took a little more time/work to find the required boost pressure
that's how it was explained to me anyway when mine was being mapped!
the in gear boost thingy is something that you could use to say have a lower boost for the launch gear to avoid to much wheel spin etc and then have it come in higher on the next gears
the other nice thing about the apexi is it 'learns' your cars characteristics too so it smooths off the boost spikes over time once it's used to it etc