Probably the best way to learn how/when to use midi CC is to learn the synth you are using. Load a patch and record something. Now rewind and start moving the mod wheel. Do the same thing with the pitch wheel.
Those two controls are easy, and mostly easy to grok, unless you are using a high-end orchestral library, then things get tricky. The other thing to learn is easiest if your controller has at least one knob on it that can send midi. In synths like Kontakt, you can playback what you recorded, and while it is playing, move various controls in the interface with your mouse. When you find one you would like to automate, right-click on it, select "Learn midi cc", wiggle the know on your controller, then record these as another pass. Make sure you are recording using "Sound On Sound". If you want to reuse the knob to automate a different control, make sure you right-click on the first control and select "Unlearn".
If you don't have a hardware knob, you can record these movements with the mouse by moving the controls in the interface, but it's a whole lot less fun.
Regards,
Dan