Do you mean to create a flight plan for FS and have FSNav follow the your route?
If so you can fo it using FSBuild. FSBuild is an application with which you can create flight plans statinh your departure and arrival airports and ask it to create the route via its database or even decide the passing points. You can then export the plan in lots of different formats. In your case you could create a flight plan and then export it in (a) FS format and (b) FSNav fornat. Move the FS formatted file to your FS2002\flights\myflts directory and the FSNav formatted to youe FSVav format and you will have both FS and FSNav follow the same route.
Alternatively you can create your flight plan at FS, save it abd then start FSBuild, import the FS plan file and export it in FSNav format. Move the last one to your FSNav directory and you are ready to go.
In both the above cases the default ATC will be accordingly to the common (FS and FANav) routing. Also if you select in FSBuild to take into consideration the altitudes the ATC's instructions regarding descend will be according to those.
FSBuild can be found on the internet in versions 1.x (freeware) and in versions 2.x (shareware). It also important keep updated your FSBuild and FSNav AIRAC databases. A good source for AIRAC (and more) navigation data patches can be found at
http://www.navdata.at/I hope it helps.