Just so I get this straight.

[DarkSora]

I have, The Fourth Age, The New Shadow: Version 2.0. Patches 2.5 and 2.6. and what appears to be of The New Shadow, War of Man. Is is possible to still play BI if you have Fourth Age installed? Is there any type of shortcut extension that I have to edit to play it because I copied my BI folder and installed Version 2.0 over it. After it was done, the shortcut didn't run at all and I got a CMD box on my desktop loading TFA data....

[Aradan]

The only think you should do is read and follow the very detailed instructions.

A) FATW is a fully modfoldered mod, which means it does not affect AT ALL your vanilla BI.
B) You don't need to copy anything if you are using the automatic installer version. Simply run the installer and point it at your main RTW directory. The programm will take care of everything else and create a shortcut on your desktop for FATW.
C) As the instructions again clearly say, the DOS window is supposed to be there, as it performs an necessary operation in order for you to be able to play afterwards. Don't shut it down manually at any point and let it do its job - after 12 mins (more or less) it will stop by itself and you'll be able to play.