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Welcome and thanks for the question. There is a lot of info to learn on this subject but here is the basic concept.
When GM makes the factory "tune" for your car they take into account all the different variations from engine to engine, car to car etc then they put a factor or safety or design margin on top of the fueling and spark to make sure it never blows up with the factory tune. The stock tune is a one size fits all if you will, its meant for all LS3s, v6s, L99s for that model year, build period etc..
When you "tune" your car what you are doing is taking out some of the built "fluff" or margin in the tune, but you are doing it systematically and accurately (if you know what your doing) by using a program such as HP tuners to read the outputs of your vehicle sensors under different driving conditions, WOT, part throttle etc. Then you take this feedback and compare it to what the tune is asking for (ciommanding if you will) and remove the error. What this does is match your mods (or even a stock car can benefit) to what the computer thinks is going on in the engine.
Example: you install a CAI and long tube headers, well your car is now breathing easier and with greater volume of air. So the little thing in your intake called a MAF (mass airflow sensor) is reading MORE air (frequency in Hertz) than the computer thinks should be there. Now the computer can compensate for this over time (it learns via fuel trims) however by "tuning" the maf to this new mod combination you take out the learning loop the computer has to go through and thus get better throttle response and more power when in WOT, which makes you a very happy camaro owner.
That is just one way tuning helps, there is many others such as torque managment etc...
So way back in the OBD I days (1980 -1995) you could get a "chip" from aftermarket companies (it is really a Memcal but whatever) which did this for you. all you had to due was pop it into your cars ECM.
Todays version of this is a hand held tuner you plug into your cars diagnostic port (drivers side under steering column lower dash area) and "flash" the computer. This is what most people call a "canned tune" which is better than stock but suffers the same limitations as a stock tune where the aftermarket company made some performance changes but has to keep margin in there to account for all the car variations for the model in question.
The only way to make the most power for YOUR car is to take to a reputable tuner, or learn to tune yourself with a wide band oxygen sensor and a tuning program which allows you to adjust all the engine, fuel, transmission parameters yourself. EFI live, HP tuners are a few that are more popular.
To answer your original question, yes having you vehicle tuned AFTER installing your mods is the best way to get the most out of your car. Otherwise your tune will be "off" or will have error in it after installing these mods.
Hope this Helps,
Ken
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