I would refer to this link in this forum whiches discusses this somewhat:http://www.rpgrevolution.com/forums/index....c=52753&hl=
In a nutshell, though, the swaps take place during actual game play, not editing. In other words, when you swap to edit one map, all maps will show that swap. So whenever you want to go back and forth between different maps using different tilesets, you must swap the profile each time. Tedious indeed, but that's how it works. However, as long as you are saving the swaps in the MAP ID of the SwapXT program, it should work when you play the game.
There's a youtube video that helps with this as well.