Find the FS2002/02 row in the Export Directories table, click on the 'Browse' button to find and select your FS2000/02 folder. Press 'Ok' when done.
Go to the 'Settings' tab and press the 'Save Config Options' button.
Shut down, and restart Fsbuild2 for the new settings to take effect.
Go to the 'Build Options' menu, and select the 'FS2000/02/04' menu item.
Build the route, the flight plan will be exported to your FS2000/Pilots, FS2002/Flights/Myflts or /my Documents/Flight Simulator Files folder (FS2004).
It is important to only select the FS 'Root' folder (ie the main MS Flight Simulator Folder folder where the FS*.exe file resides).
It is also important to 'restart' Fsbuild2, as the settings will not take effect until the next program start.