It's added to injector pulsewidth always. As a percentage, it has most effect at idle (low pulsewidth). However, if you have a very large injector (like 120's and up), that operates at low pulsewidths much of the time, then it can be significant when cruising around.
Your method of tuning will work. However, I typically have the deadtime, voltage compensation, and low pw table (if used) set up pretty close.