Long Distance Flight Scheduling...(?)

Greetings VA folks...I am working on a schedule for a VA and have a curous question as to scheduling. For those of you who do long-distance runs with your aircraft (5000+ miles), how do you come up with the times for your flight schedule. I have used both FSNavigator and FSBuild to create flightplans for my aircraft, but I know those programs do not take into account the typical winds you see in long flights. Do you all simply FLY each leg to determine the times, or do you let a scheduling tool assist you?Thanks for your input!-Greg