There isn't really "one way" for doing this, different people use different methods, both in their approach for tuning and what they actually do with the variables available.
Some people might tune generally, to try and make a car "ok" for a many different situations as possible, others might fine tune a car or a single purpose, or situation i.e. a certain track and certain regulations (PP or power/weight).
Some people might make small adjustments to a stock (custom suspension and LSD), other might change everything, some ill do this straight away - even before they drive the car, others might drive the car for a few laps, or even give it a thorough work out in different situations.
It's very easy to end up going round and round in circles with a setup or single car - there's cars doing this to me right now, I change it, then change it back, then try something new, then change it back, try something new etc etc etc and it still wont do what I want. Then again, there's cars I apply a formula to and are done in 60 seconds - they have turn in, grip, balance, even tyre wear and tyre heat and respectable lap times.
To try and avoid the situation of going round in circles (this might not work for all, as said above - everyone has their own "way"), start with the golden rule - KEEP IT SIMPLE:
Stick to 1 drivetrain, maybe FR
Split the tuning into 2 areas - suspension LSD
Take 3 copies of the same car, one stock, 1 with custom lsd and another with custom suspension
The reason for this is that when you adjust either the LSD or the suspension, other variables won't be affecting your changes, so what you do, and how this either works or doesn't is directly related to your changes.
Use a car/tyre combination that is fairly neutral and not to planted / grippy, again, - so you can feel the difference in traction with different changes.
General hints / tips:
Have realistic goals / achievements - dont pressure yourself into "learning setups in a week", I'm still learning after years of tuning. As the game (and it's physics) change, you'll need to adapt too, dont try and run before you can walk.
Be honest with yourself - can you run consistent laps, time after time - if not, can a friend(s) help you with this.
Would changes to driving style be as helpful as learning tuning / setups i.e. if not doing so already, changing / learning to trail brake and feather the throttle / gas might be a big help?
Use different tracks to test your findings.
Use information in the game i.e. tyre indicator - this tells you your tyre heat and tyre wear, having even heat and wear is a realistic goal to tune to (especially with FR cars, which is why they're a good starting point). Likewise, having uneven tyre heat and wear can potentially tell you where a problem might be. So when you are doing your testing, always have tyre wear on.
Deal with what's infront of you i.e. in the game, dont learn real life tuning, GT isn't the same, in some cases, it can be the opposite.
Don't use drivings aids, ballast or too grippy tyres - these can all "hide" or overpower setup changes.