One your CG is set, and you have tuned your low-rate elevator response so that you are landing smoothly, you can move on to tuning your controls for performance and optimizing your aircraft for you.
Roll Rate (aileron throw)
There is nothing critical about aileron throw. Your low rate should be low enough to fly smooth landing sequences and correct for wind accurately. Your high rate could be set, as many people's are, to max out the roll rate at high speed...but I don't recommend this. We all know the guy who just wants to show off that his plane rolls like a drill...but can he actually use that high roll rate to do anything? As you learn to fly more complex maneuvers, you will be required to coordinate your elevator and rudder as the airplane rolls (rolling loops, harrier rolling, etc.) When you are ready to actually work on such figures, make sure you high rate aileron is set low enough that you can keep up with the roll rate when learning to coordinate. Typically, no more than 35 degrees is necessary on high rates. Use sufficient exponential so that you are smooth on this control. Typically this is in around 20% on low rates and at least 50% on high rates.
Elevator Throw
This is critical. In our Extreme Flight and 3DHS branded manuals, we always recommend at least 45 degrees of high rate elevator. This gives you enough elevator authority to be able to instantaneously stall both your left and right wing, this is how you convince the airplane to stall straight ahead and you can power through the stall and start flying 3D.
We always recommend a low rate throw 15 degrees or less, but this needs to be tuned for the individual pilot. As mentioned in the landing article, you need to adjust your low rate elevator so that you can really fly a string-straight line down low near the runway without drama. This is the most important use of low rate elevator for the beginners because it allows smooth landings. Later you can get into precise tuning of low rate elevator to achieve a precise radius in precision figures...but get your landings smooth first. If your airplane is porpoising up and down when you fly close to the ground and you can't draw a straight line, you need to turn down your low rate throw and possibly increase your low rate expo.
Use sufficient expo on elevator to smooth out both rates, high and low. This is typically 20% or so on low rates and at least 50% on high rates. I prefer 70% on high rates, and recommend people start there.
Rudder
This one is trickier.
For a 3D plane, we need sufficient rudder to allow us to shove the tail around in rough maneuvers like hover. That requires a LOT of throw. 40 or 45 degrees. However, when we are flying the harrier maneuver, we really need to be smooth on the rudder or it is easy to cause a wing to drop or make wings rock. Rudder exponential, therefore, is critical. We need enough expo that we can precisely add very small amounts of rudder in harrier, while being able to command full rudder throw at a moment's notice when we need it. This requires experimentation. I fly 75% rudder expo, and I recommend beginner start around there. You can always reduce it.
You can set up a rudder low rate if you choose, but for a beginner it's much more critical to get the expo right. If so, one rudder throw level is almost always sufficient for everything you will be doing. Later, you can optimize a low rate rudder for precision aerobatic figures.
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Things you should NOT change.
We all know what the internet is like. It's really boring if people were to simply post "I'm practicing my landings". No, we're techies and so we talk tech. What people are lured into doing is modifying their airplanes, almost almost always for the worse, when they should be concentrating on building flying skills.
What you should not change are the designed aspects of your plane. I'm presuming you have a very high-quality, proven design.
As an example, people on the internet are forever altering their right thrust value. This is the amount your motor points off to the right on your airplane. Don't ever change this. 99.9% of balsa ARF aircraft have 2-3 degrees of right thrust built into the airframe and this is just fine. Over the years, I've used 2.5 to 3 degrees and so have all of our other designers, on the airplanes I was involved in, and it works fine. There is no flight problem which can be fixed on a typical 3D airplane by changing the right thrust to be outside these limits...but if you follow the wacky RC internet, someone somewhere is *always* doing this and (blissfully unaware of how dumb it sounds) claiming it fixed their airframe.
The background is this: Right thrust is only "correct" for one particular prop and at one particular throttle setting and airspeed...for every other condition it is "incorrect". But, it's close enough that an approximate setting (2-3 degrees for our typical aircraft) works transparently for almost all flight conditions.
Every now and then, some new person will realize that adding more right thrust allows them to hold less rudder in hover, and they think they've discovered the secret of the universe. They write angry letters telling me that at 6 degrees of right thrust, the airplane hovers better and how could I have missed something so obvious. They never realize that the airplane now flies a giant circle at high speed and requires them to hold left rudder to go straight.
Moral of the story: Don't change any of the designed-in attributes of your airplane. Learn to fly instead of messing with the airframe. We, and our team pilots who win national events with our aircraft, fly them box-stock. We use all of the hardware that comes in the box, and we use the CG and throw setting printed in the manual. Don't be taken in by someone on the internet telling you he changed some design aspect of the plane and now it flies much better.
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The final moral:
Get a proven airplane from a reputable manufacturer.
Use the recommended equipment.
Assemble it according to the manual.
Set the CG carefully at the recommended forward setting on your workbench.
Check your controls and power system carefully, if it doesn't seem right, don't fly until it is.
Get a buddy to double check your controls are going in the correct direction.
Fly a short maiden flight, grossly trim the plane, and land on low rates.
Calculate your flight time.
Set your CG in the air using the roll-inverted test. Make it slightly nose heavy...maybe a bit more nose-heavy if you have trouble landing.
Follow the landing instructions.
Tune your controls for your desired feel, especially taking time to set your low rate elevator for smoothness in landing, and your rudder expo for a combination of power and delicacy that will allow you to progress in both hover and harrier.
Don't get taken in by bright ideas to change your aircraft around, instead practice your flying diligently.