1. Select Fleet & add/subtract ships.(gives X, Y, Fuel, Cargo space)
2. Adjust Pop/mineral levels.(start with whatever is in the fleet)
3. Select end point.(Planet, Fleet, XY)
4. Calc the optimize jumps.
5. Break the fleet down by ship type.(only 16 possible, easier then grouping by engine).
6. For each ship type
6a. Do one year travel.
6b. Adjust Pop & Fuel(adding or subtracting as needed).
6c. Do again until you reach the end point.
7. Put the fleet back together
8. Did we have enough fuel?

That's basically it, a lot of details left out.