Ok, first, if you are producing 20000 intel points per turn, then you need to spend them all or they are wasted. If you have 1 project which costs 5000, then that project will be completed and you will have 15000 left over. Like Research, you can divide points evenly (bad idea because points are frequently lost when completing projects) or you can have projects be done sequentially. If you had other projects after (to the right of) the first 5000 point project, they would consume their required points and be completed until the Last one was partially completed when the Last of your points for that turn are expended.
Now for Counter Intel...
As attacks come in, they are blocked with CI points. CI level 1, 2 and 3 blocks points as you read in the FAQ. When CI points are used to block an incoming attack, they are deducted from the CI project. When the Last CI project is lowered to the point where it cannot stop the following attacks, the incoming attacks will succeed. I *think* that any points you are putting into CI for are particular turn are added to your CI project before (not after) the incoming attacks are attempted to be blocked. Whatever you do, DO NOT COMPLETE A CI PROJECT. If you do, you will lose all the accumulated points with no benefit.
Hope this helps.
[edit: beat by a speedy typist

]
Slick.
[ April 19, 2003, 01:51: Message edited by: Slick ]