Most commercial airliners use the Flight Management Computer.  The pilot inputs the waypoints, and presses "Execute", and the plane does the rest.  Unfortunately, I have yet to find a downloadable plane that has this amazing feature.  (Though I did have a payware add on for 98 that had it...) 

Maybe someone else knows of an aircraft or utility that will do that for us...

To answer in a more general way, from what I understand entering the waypoints into the FMC is much like creating a flightplan with the default FS planner and flying the GPS route. Usually this route will be based on high altitude airways although sometimes it can be a direct route. I think the autopilot is slaved to the FMC, the pilot isn't actually flying the VOR radials that define the airways. Most pilots say they fly manual until they get to cruise then hit the buttons and go back to manual for descent and touchdown. At busy airports there are departure procedures to send all departing flights in a uniform fashion and arrival procedures to merge flights into a line and then they receive ATC vectors for the runway. (DP and STARs)
It's difficult if not impossible to make STARs work in a default IFR flightplan in FS. The ATC will always start vectors at least 50 nm out, so you would not get to really fly the arrival precedure. Plus they would get on to you if you descended and then tried to re-contact them when you were close, they would say to climb back to your filed cruise altitude and if you didn't they would cancel your plan. I think the FS2004 will be better at this.
Did I miss anything?

It really doesn't matter. GPS direct routes are coming into the picture these days, but I think currently airlines pretty much stick to the High Altitude airways which will create a flightplan utilizing a mix of VORs and Intersections as waypoints, the FMC will incorporate GPS fixes as waypoints. Sometimes you have to add or delete a VOR waypoint to suit your departure or arrival, depends on what you like. On the FS cockpit panels there is a NAV/GPS switch and when it is on GPS then the autopilot will follow the flightplan (you have to enable NAV or VOR hold).
I like to actually see what VOR radials define the airways and track the radials while checking my progress with the GPS, but I'm most certain this is not done by airline pilots.

It sounds like you are asking basic VOR navigation. I guess you don't want to fly like the real airlines! only kidding. This is what I do:
-File the plan and look at the heading to each waypoint
-If I'm flying to a VOR, I track the radial that is the reciprical of the heading in the planner. (ie, hdg170, track radial 350 to the VOR)
-If I'm flying to an intersection, I track the radial AWAY from the VOR I just left (ie the radial and planner heading will match)
- If there are more than one intersection in a row it can get tricky, but usually they can just be ignored and used as a method of determining progress.

The VOR frequencies are under the map view (world menu). Intersections do not have frequencies, they are an imaginary point in space where two radials from two different VORs intersect. I find them difficult to locate on the airliners because you have to use both NAV radios, and the NAV2 on airliners is just a pointer. It doesn't really tell you if you are on a radial.

Did I confuse you? You can learn here:
http://www.navfltsm.addr.com/vor-nav.htm

Absolutely. I know what you meant.  

I've met and talked to a few commercial pilots, and have known a few Air Force C-5 drivers, and they all seem to have the same view of they're roles as pilots. Flying the plane isn't exactly the same as piloting the plane, to them.
Piloting the plane involves all their technical training and expertise to do they're jobs.
Flying the plane is like driving the family station wagon. Period.

God love 'em!  

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That's a good one!

yes now most aircraft got a nav computer but as say my father who is pilot on A340 Fly with nav computer is not fly

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Guess what i found in my FS2002 Gauges folder. Thats right, an FMC for the 777. Probably got it from one of the add-ons ive downloaded over time.