Grudge, if you've gotten so far as to unzip the patch into the EU directory and run patch.exe all you have to do now before each game is run the file IGCConfig before you play. This file will now be in your EU directory.
I created a shortcut to this on my desk top.
Run IGCConfig. You'll get a window with 7 boxes on the left. Simply click the arrow and a list of coutries in each box will pop up. You can now chose 1 country for each of the 7 boxes and these will be the countries you can play in the IGC! They will also be the ones you can't annex.
IGC 1.09 should default with the standard countries already selected. If you just want to play 1 country ie Genoa, find it in one of the lists and chose it then leave the 6 other boxes as "none" or fill them with countries you don't want to be annexable.
Now click "apply". Click "quit" and then run EU like you normally would. Chose the "IGC" scenario and the Genoa shield will be there wating for you to select it!
In summary if you want to play IGC, you now need to run IGCConfig 1st, close it and then run EU.
It really has been designed to be simple! Good luck.