When Counter Intel is almost finished I just replace it with the fresh one. Just don't want to risk having troubles
And yes, turn Divide points off. All your offensive projects must be in front of Counter Intel project and MUST be 'finishable' in 1 turn _AND_ there must be some points left for CounterIntel. Otherwise it won't work and all the enemy's intel projects will hit you. Usually it is very painful (gues how I found it out ...
).