The general rule of thumb is to install contents from folders into other identical folders, overriding files in those folders. If a folder doesn't exist that corresponds with a folder to be installed, a similar procedure should be applied - create a folder with an identical name, and then drop the relevant files inside.
Copying over entire folders can be risky since not all folders contain all necessary files.
Another tip, if you are running different theaters in FE2 (Middle East, Eastern Front, etc.) is to make several copies of your ThirdWire folder (the one in your "games" folder in Windows, not the actual game contents folder) - and then to mod each of those theater folders....then you can simply swap in/out the theaters you want to fly by naming the folder you want to fly as "ThirdWire" (without quotation marks) and making sure that it's in your games directory of your user account in Windows.
Von S