Hi Morten.

This is what I do.

I listen to the ATIS at my departure airport (or the tower if there is no ATIS).
Complete the flight plan without the SID, STAR, TRANSITION & RWY, then copy it to RTE2 and don't touch it.
Use the Map to see which departure runway is closest to the Gate you are parked at, and then set up a departure using that runway (you could also ask for taxi clearance so you know exactly runway you will be using).
Put You SID into the route (you can add a STAR TRANS and RWY if you want to, this will give you a better idea on fuel required) and you are ready to go.
Once you get near the Arrival airport, if you need a different STAR, TRANSITION and RWY, you can add it to RTE2 (rather than fixing the changes that would occur in RTE1) and finish your flight using it.
I'm assuming that you know how to switch routes mid-flight if needed.

Mark