Counter intel only works while it is in PROGRESS, not once it gets finished. So if you haven't started one, START IT NOW. It's only when its FINISHED that it doesn't do any more good. When the first one finishes, start another.
I would assume just start on the highest level of counter-intel you have, and keep building more intelligence centers to increase your intel points.
I couldn't tell you exactly how counter-intel works, or what's the difference between counter-intel 1, 2 and 3, or how many of what level of enemy projects it will defend you against (I don't know if anybody's figured it out yet
), but that's your best shot.
Also, if you have (or create) a partnership treaty with an ally, they will share a portion of their intel points in addition to sharing research and resources.
Good luck, and I also like the idea of waltzing into their systems to blow them away for stealing your ships!
[ 09 December 2001: Message edited by: MegaTrain ]