Assume an install of the Mini-Tweaker in
C:\Program Files\SH3 Mini Tweaker\
With your Tweak Files located in
C:\Program Files\SH3 Mini Tweaker\Tweakfiles
Here is the most important thing to know to get started with the program.
The "File You Want To Tweak" is determined by two things.
1. The game folder.
If you have installed SH III, the game folder is read directly from your computers registry. This is the directory that contains the Data folder, C:\SH3 on my computer.
If you do not have SH III installed, the application will ask you to select an alternate game folder.
In either case, you can reset the game folder once in the program.
2. The relative path to the "File You Want To Tweak".
This is set by a parameter in the tweak file you load. For example my tweak file NSS_Gato.zon.txt contains the line:
PATH=..\SH4\MODS\My_Uber_Subs\Data\Submarine\NSS_G ato\NSS_Gato.zon
.................................................. ............................^ no idea why this space is here
Notice how I first back up to the root from my default game folder of C:\SH3, then change up into C:\SH4\... this means I never have to change the game folder in the tweak program. I had to edit all my tweak files to do this however. If you would rather not do that, then you can simply reset the game folder every time you use it.
Also notice that I went into the \SH4\MODS\ directory to modify files - it is not a good idea to edit in the live Data\* area.
The game folder should be set to a folder that contains a Data folder, the tweak file PATH should take care of the rest of the path (relative to the game folder).
Hope this helps, I have seen a lot of confusion on this topic lately.