Firstly, both the .Net version and the Java version gives the same output (mostly, but still readable by Mede8er). Secondly, yes, it's as simple as point and click
My app will take the XML/NFO file and convert to Mede8er compliant XML in the same folder where the XML/NFO file is located, so your directory structure would be fine. However, I recommend testing on a small sample folder to make sure the NFO files are read correctly. If they are not read correctly, feel free to send me a few sample NFO files and I will see how I can read the NFO files to give the correct output.