Yes Erik, I've the bible and I found the information 'How the interrupts are handles'. It's answering to my question.

Sometimes it's confusing because I'm using also Motorola HC08 for which there is a specific datasheet for each peripheral.
When looking for the information concerning the timers, I was looking in the philips semiconductor website for a document dealing with timers but without any success. I have to recognize that I've forgot the bible on my harddrive ....
I do apologize for this.

To answer myself, here is the solution I plan to implement to generate a long accurate pulse.

I will use Timer2 as Output Compare to generate a pulse burst with an accurate period (for the example let's take 100 pulses each 10ms).
Then I will use a external counter for divide this burst by 100. I will have then a 1s accurate.

Of course I will use a ratio of 128 instead of 100....

This calibrated pulse will be used as timebase for a frequency measurement.

Stephane