Tuning for noob(s) required

GUTCH

Ok so I've been doing a hell of a lot of research both on the forums and on the internet in general in relation to tuning. Yet it still isn't 100% clear to me.

People here mention they have their cars tuned by Uprev, Cobb, etc.

Do these places simply work with the existing factory software the car comes with or are they adding their own? When is third party software required? Is a flash part of a tune or a separate process entirely?

I'm essentially confused as to when a tune involves working with the car, meaning essentially labour only and when it involves a product such as software as well.

If anyone could spell out all of the above (and more?), it would be greatly appreciated. Perhaps something like the "Forced Induction for Noobs" sticky thread.

Thanks in advance.