There isn't a way to do this simply.
Either you first select a direct GPS then drag the red line to VORs and intersections to match your flight plan.
Or if you know the exact locations of intersections, you can create the flight plan in notepad, and save as *.FLT. Take a look in My Documents > Flight Simulator files to check how does a FLT look like. For example:
[flightplan]
AppVersion=9.0.30612
title=ESSA to LPPR
description=ESSA, LPPR
type=IFR
routetype=3
cruising_altitude=30000
departure_id=ESSA, N59* 39.13', E17* 55.86', +000124.00
departure_position=GATE 6
destination_id=LPPR, N41* 15.77', W8* 41.11', +000228.00
departure_name=Arlanda
destination_name=Francisco Sa Carneiro
waypoint.0=, ESSA, , ESSA, A, N59* 39.13', E17* 55.86', +000124.00,
waypoint.1=ES, DKR, , DKR, V, N59* 12.43', E17* 0.72', +000000.00,
waypoint.2=ES, ELPAX, , ELPAX, I, N58* 5.73', E15* 16.40', +000000.00, UN872
waypoint.3=ES, TOKSI, , TOKSI, I, N57* 9.34', E13* 54.66', +000000.00, UN872
waypoint.4=ES, MISMA, , MISMA, I, N56* 38.48', E13* 12.17', +000000.00, UN872
waypoint.5=ES, SVD, , SVD, V, N56* 10.13', E12* 34.43', +000000.00, UN872
waypoint.6=ES, KOPIM, , KOPIM, I, N56* 8.03', E12* 29.90', +000000.00, UN872
waypoint.7=EK, LASGI, , LASGI, I, N56* 6.80', E12* 27.27', +000000.00, UN872
waypoint.8=EK, NAROL, , NAROL, I, N56* 0.35', E12* 13.50', +000000.00, UN872
waypoint.9=EK, DOBEL, , DOBEL, I, N55* 36.36', E11* 23.40', +000000.00, UN872
waypoint.10=EK, ALS, , ALS, V, N54* 54.32', E9* 59.60', +000000.00, UN872
waypoint.11=EK, KESUR, , KESUR, I, N54* 50.43', E9* 53.25', +000000.00, UZ703
and so on
