is it fuel or timing and fuel?
if it is just fuel you will want to try and modify the map so that you are running a safe afr for any given boost pressure you plan on running. A "safe" afr is determined by a number of things inlcuding but not limted to the type of gas you use, the temperature of air the is entering the engine and how much load is on the engine.
A safe bet would be to tune for 11:1 AFR on 91 octane while in boost and see how your setup likes it. If you have a decent intercooler or 94 gas then move towards 12.2:1 under boost.
if you are just using the afc then thats mostly what you will be doing. work off the base map and increase/decrease fuel values in the cells so that the afr stays as close to the target value under boost as you can. easiest way is to ride shotgun with a laptop and have someone else drive around for an hour or so while you make changes to the cells.
i cant remember offhand as it has been a few years since ive tuned a "stockish" setup, but I believe under ~4000rpm the stock ecu is still in open loop mode and will be running leaner than you think you should be, then there will be a noticeable switchover as the rpms increase. im sure someone here currently running an afc can give you more/correct info on this. it is a switchover point from open-close loop. might make tuning a bit confusing if you arent aware of it, i know it did for me back in the day on my first tune.