The program itself is fairly simple (when you know how)
If you download NVDrifter's mod tools:
http://www.subsim.com/radioroom/showthread.php?t=109854
you can install mini tweaker anywhere. Once that's done install the tweak files into the \Tweak Files folder. To use it for SHIV when you start Tweaker it'll complain (cos it was made for SH3) just click the little button (top right) under "Locate Alternate Game Folder" and select your SHIV directory. Then you just have to load a tweak file and edit the values.
If you are looking for more precise instructions on the actual tweak files the best place to ask is in the threads related to them (just do a search for "Tweak" on this forum.