From what I can work out : (DISCLAIMER - I DON'T KNOW SHITE)
First there is the intial wiring of the ECU / SAFC / Fuel Computer -whatever - If plug and play no need to worry
There is your initial setup: eg Injector Sizes, AFM sizes and Voltages (and MAP sizes etc on some ECUs)
Then there are things like idle, cold start, etc
Then there are 2 important maps you need to configure.
1) Fuel vs load vs revs
2) Timing vs load vs revs
These two maps form a sort of 3D graph of your setup. You change something in one axis - it may affect the other.
You need to monitor your A/F ratios, Your knock, (multiple ways/methods) whilst tuning.
You tune so your knock stays acceptable and the your A/F ratios (depending on load) are acceptable.
There is prolly much more to it than that -
I'm quite interested in this sort of thing -
The problem is that tuners who know what they are doing are not very willing to share info on a public forum.... (does them out of a job)
I plan to dip my toe in the water - by building a fuel computer for the Gloria and doing a road tune with a a wideband A/F meter.....
Anyawy - you need a bit of equipment and prolly a dyno and spend a lot of hours on it before one could call themselves a capable tuner.....
Hope that adds to the discussion - and maybe someone can elaborate and add to it
Cheers,