Yes, mini-tweaker modifies the actual game files. The text file that you load (and can be stored anywhere you want to keep them) is just the template that allows the tweaker program to modify the appropriate game file. If you load the text file for the GUNS_SUB.zon file, you would then be modifying your boat's guns, and so on.
One other thing you should do is to remove the copies of the file that the tweaker program makes. While I have never actually had the problem myself, some modders have said that the game will stubbornly retain it's use of copy (which is actually the original) and not load the modified file.
As always, back up your original files before playing with modifications. Unless, of cource, you really like to uninstall and reinstall your game from time-to-time...
Bob