What Roy means is that you would have different characters. One for the Capital Wasteland and one for the Mojave.
When you travel to the other wasteland you would change characters and your "other one" would become a follower.
So when your Lone Wanderer travels from the CW to the Mojave for the first time, you would make a new character (Courier) just like normal FNV and play with it, then you could find the Lone Wanderer somewhere and he would join you as a follower, then when you travel back to the CW, you would control the Lone Wanderer and the Courier would become a follower, and so on.
