How To Handle Creating Directories

I'm creating that sets up project directories based on a template and also allows users to select folders from the template to add to a selected path (their project dir). I've got everything figured out as to creating the directory initially except for 1 thing that ties into another (stick with me here). I'd like to create the directories based on a text file or some sort of config file. Essentially, I would have a text file that contains lines like:

oot
ootsub1
ootsub2

[code]....

etc. Then when I create the directories, I can create them based on these lines. I think I can figure that part out myself. Where I'm stuck is on comparing the selected dir to the template dir. Right now I have a treeview control with checkboxes that is populated based on a path that the user selects from the folderbrowserdialog. What I need to do is compare the selected directory with the directories in the text file and if the directories exist (match) then they are checked. If they don't exist in the selected directory then they are unchecked.

If a user wants to add a directory from the template, they check the box for the dir they want and uncheck the boxes for the ones they dont. Then hit apply and the app will either create or delete the checked/unchecked dirs. What's the best way to handle the template dir? Should I do the text file thing or should I simply have the directory structure setup somewhere where the app can copy the dirs from the template to the selected directory? Or should I use an ini file? I want to make the app flexible so that down the road, if they change the template layout, or where the template lives, the app can be told that. So I need to add a way for the users for example to choose the template directory (but not everytime!) or specify the path that the template dir txt file lives.