My advice:
Don't bother with the migration tool in this circumstance. Why? Because you will not understand how to configure things in a meaningful way, and if you attempt to migrate a production network, you will be pressured to make things work and not understand when they dont. To answer your question: The MM and the backup MM replace the Master and Standby hardware, except they don't terminate any access points.
Create your MM and maybe your backup MM on a Virtual Machine. Create a folder under MD and create your controllers and WLANs there. This will allow you to configure everything from WLANS to interfaces on controllers without having those controllers online.
When you are ready to migrate your 6.x controller, you will need a console cable. Upgrade to the latest 8.2.x.x and reboot. The console will allow you to point it at an MM. It will register with the MM and get its entire configuration.
That is a general overview of what you would need to do. For specific instructions, please look at the videos in their entirety here: https://www.youtube.com/playlist?list=PLsYGHuNuBZcatGA1POy6iVpVlDTLYzNFE before you do anything so you understand fully what you need to be effective. It is worth staging the MMs in the lab first with a test hardware controller to understand the procedure to understand where everything is. The migration tool is NOT a substitute for fully understanding how things are different and what you would need to do..
Lastly, ask questions on the forum here and we will guide you through the steps in your lab, until you feel confident enough to do everything yourself. There is quite a bit to understand, so I would migrate an active network in steps, after going through configuration in the lab...