Unfortunately Scotch you (a player) can only program one IFR flightplan at a time using the default FS 2004 Flight Planner.
Say for instance that I want to go from Dallas Love Airport (KDAL) to Albuquerque Intl. (KABQ). On the way I want to stop off at Abilene Regional (KABI) and then to Lubbock Intl. (KLBB). On the return trip I want to fly directly from Albuquerque Intl. (KABQ) to my home airport Dallas Love Airport (KDAL).
To accomplish this I have to create four different (Direct GPS) IFR flightplans:
1.) KDAL to KABI
2.) KABI to KLBB
3.) KLBB to KABQ
4.) KABQ to KDAL
There is a Payware (well it MAY be free -- every 30th download is already registered and does not require you to purchase a registration) Add-On Utility for FS 2004 called FSNavigator which is now up to Version 4.6.
I believe that this program will enable you to plot any type of IFR Flightplan that you desire, including multiple waypoints and cruise altitudes. You can download it here:
http://fsnavigator.com/Just click the Download to get it. During install it will tell you if your copy of FSNavigator is good for only 20 FS 2004 sessions (after which time you will need to purchase a registration key at a cost about $40.00 US) -- or - the installer may tell you that you just downloaded a free registration!
I hope that this answers your question.