I dont see where you would run into any problems. The default folder where the script makes the categories is simply "category". I guess the only problem that could arise is if you have free sites in a folder called "category". If you do just change the folder to make the categories to a folder you dont already have.
I mean am no expert at all, if you have any questions I would highly suggest you talk to the xpowerlink guys, they were more than helpful with me when I was figuring the script out.
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