You adjust what you changed out.
If you changed the injectors, you adjust injector parameters
If you changed intake, you adjust the MAF scale.
If you changed both? You put the intake back to stock and scale the injectors with the stock MAF, then you put the new intake back and scale the MAF... or you just guess at the injectors and then scale the MAF (which is what most do, since if you get the injectors close enough, the MAF can get you the rest.)
Once the injectors are close and you have a reasonably flat MAFv curve as far as latency / flow scaling adjustment, you can use the MAF scaling to take more of the "wave' out that you can't adjust with injector parameters.