Of course it doesn't matter what you do in-game, you can't break anything. But in real life you would only use the independent brake for light engine movements or when coupling to a rack of freight cars. When you are hauling a consist, you would use the train brake or dynamic brake or a combination of the two. I'm speaking of US freight practice. Other countries may be different, especially if they have a combined power/braking handle.
Crosstie He's not asking about the independent brake, but about usung train brake and dynamic brake independently I believe it can be done, after all, the AFB does it!
The electric brake is meant to be used alone or with the air brake so you can use it how you want. Its main purpose is to help trains descent on long grades where constant braking is required. The constant use of air brake can result in excessive wear, over heating of the pads and loss of braking force, running out of air in the main cylinder. Since electric brake changes the magnetic field inside the traction motor and slows the rotor and wheels is basically free braking and can be used alone or with the air brake depending off the requirements. A lot of trains already use a combined form of electric and air braking since electric is also highly efficient at high speeds while dropping efficiency at low speeds.