Hello! I recently got Independence War and am using a keyboard joystick combination. I have wanted to modify some of the buttons on it but am unsure as to where I do so. Can it be done through the game or do I have to go into the program files and change it there? I am using a Logitech Attack3.
Any help would be greatly appreciated.

Unfortunately it's not possible to change the joystick buttons in-game, but you can use third party joystick apps to do it.
In particular there's a program called xpadder, which allows you to bind keyboard commands to joystick button presses.

There is also an application designed especially for EOC called ....(Wait for it)
EOC Key Binder!
I have attached it here. All you need to do is rename the JPG extension to .EXE.
Advanced users can create their own custom control configurations if they wish, by creating their own control config ini files.
You can bind any joystick or mouse axis, and joystick, mouse or keyboard buttons to any of the game's commands. For example, if you have a second joystick, you could configure it to control lateral thrusters for extra flexibility in combat.
Details of how to do this are in the EOC readme file supplied with the game.
This program was created by Peter Tan to help you create and edit control config INI files. Many thanks go to him.
Please note that the program is not supported by Particle Systems or Infogrames or GOG. Please send any comments to the author.

If RaptorEV5 is asking about the original Independence War then that program won't work unfortunately. If he's asking about I-War 2 The Edge Of Chaos, then it's fully configurable via that program or manually editing the control ini files.

Oh snap!
I misread the original post. I thought he was asking about I-War 2.
Sorry. :(