Hi, downloading Greek flights makes me believe you are probably from Greece too (as I am).
Anyway, it seems what you need is the Project AI installers which can be found in the following link:
http://projectai.flight1.net/certified/menu.htmI assume what you have downloaded is in a format of text file. Extracting the installers to a directory of your chooice you just run the TTools.exe and select as input the text file with the flight plans you have downloaded and click on the button labeled "compile". It will update your traffic.bgl file which is your default traffic. It is a good idea to keep a copy of the traffic.bgl before.
A problem you may face is that if you have downloaded Greek flight plans (Olympic Airways, Olympic Aviation) and instal them as I described above, you will get the ATC you want but you will never see those airplanes in the airports unless you have the textures too. I would suggest you to download the flight plans from the official Project AI airlines (including Olympic Airways and Olympic Aviation) which also include the textures. I have instlead them all in my FS2002 and works perfect.
Hope it helps.