I don't know why the military is against calling 1-800-wx-brief. The guys know their sh*t. Filing is a 2 minute phone call if you have all the info available and have already checked weather and notams.
Something else to realize is that even if you're filing from a civilian field to a civilian field in a civilian aircraft, your flight plan info is very different than your ATC info. Not all the info in your flight plan can fit in the ATC system. So basically, you end up w/ three different systems. Military, FSS, and ATC.