I is something for the accountants and planners to worry about not the pilot other than to input into the FMS what he has been told to input?
No. You get the CI before the flight. However that CI is a planned figure. It is all theoretical. So if you are, say running late, you can fiddle with the CI so that you arrive closer to scheduled arrival time. ie use a higher CI. What happens on the day is that it becomes a trade between time and fuel.
You decide what fuel you want to land with, then up the CI till you get the arrival time you seek with the fuel you also want. However if the headwinds are greater than anticipated you have to reduce the CI to get the arrival time that is dictated by the fuel you require to be remaining.
Alternatively. Bin the cost index method, and put in the speed you want that gives you the arrival time with the fuel you require.
So, as the Captain what you decide to do on the day is not necessarily dependant on the required CI.
Is that clear? I think I just confused myself!
Ltt