Well here is what I read from Trey Cobb on their forum. It was very helpful and gave me the answers I was looking for.
Base Map: The permanent stored programming in the ECU for stuff like timing, boost control, etc based on the mods you have for the map you're loading. If you disconnect the battery, the base map is reverted back to. Only when you flash a base map or revert it to stock does it count towards the flash count on the ECU.
Realtime Map: A small portion of the base map can be altered with a realtime map but the variables are very small that can be changed. If you disconnect the battery, it will revert back to your base map and the realtime variables will be erased. This will not count towards a flash.
Read that long post and it will answer a lot more questions than the main website. Enjoy.