You can use either non-C-Gear abuse or C-Gear abuse for whatever you want. You can breed with C-Gear abuse (like me) if you really want to, but everyone will be flocking to Non-C-Gear because of how easy it is. Both methods can be used for breeding and capture, or whatever you want. The one exception is Dream World Pokémon, as you're required to turn the C-Gear on to access them, meaning you'll have to do C-Gear abuse.
C-Gear abuse is delay-based. However, unlike 4th gen where you hit either even or odd, you hit both even and odd meaning you have to be twice as accurate.
As for the egg thing, yes, that's true. The PID (which determines nature, gender, and possibly ability) is not set in stone until you actually receive the egg. Ability is something that's not quite understood this generation. It doesn't work like it did in gen 4.
And sorry, I don't know of any good 5th gen damage calculators.