Board Software
MSI's Command Center is the tool to use to control hardware-based features like voltages and clockspeeds, or things like fan controls or hardware monitoring. When you want to update your utilities for the board, drivers, or the BIOS, LIVE Update 6 will make sure you have the latest and even installs them for you.
The MSI GAMING APP has also been updated and is how you get to the controls for the board's built-in RGB lighting. The lighting is broken up into different areas, so you can customize the color and such of each section independently.
There are MSI-branded versions of Intel's XTU software and the popular CPU-Z utility.
Nahamic is software to control audio stuff with, and you need the SuperCharger software to enable the USB ports' fast-charge modes.
The USB SPEED UP tools will help you get the most performance out of those USB ports.
There is other bundled software included with the MSI X99A GAMING PRO CARBON; I've just chosen to highlight those I find useful and have left the rest for you to discover.