When I used to fly in FS2004 professional I used to start free flight and than switched everything off.
Next step was to save flight as default. This is important because if it will be not default it will be not on priority. But its working only on saved flight.
You didn't mentioned if you are flying in FS2004 or FSX because now I am using FSX and somehow this version seems to be doing this automatically aftew few startings from saved flight as default and if I chose new free flight its doing automatically. Notice that engine hours from saved flights will be nicely counting on and on...
One tip:
find your FSX.CFG or FS.CFG file and look for item SHOW_OPENING_SCREEN=1 , than change it to "0". This means that when you start your simulator, it will skip menu with user interface.Set up system time as default time system in simulator general preferences tab, it will load your windows or bios time and set it accordingly to the Greenwich time system. Starting simulator will skip the menu and it will load saved default flight (with your "black" cockpit) which you already saved with engines off and load it automatically with "real" time setttings.
Try connect this with real weather information gives you nice ipression of "close real" sim-flying...
PS: Sorry for my english
