Watch the youtube tutorial a couple times. I completely failed on using it my first time too...
Where I failed is: When the program asks you to save the game before swapping out, close the program at that time and then proceed. It will reload the program and everything will be properly swapped as you set it in the XT program.
It takes a bit of getting used to, but it's really not all that hard... ultimately it's like importing a new tileset and setting passabilities for each map you're swapping.