Hi Adam - there's a good barrel thread going on right now here:
You should plan on filling the barrel for extended aging. In the thread I link to above, there was some discussion about using a single batch sort of as a yeast starter in a barrel, in order to (a) build up the yeast (like a stepped starter), and (b) create a CO2 blanket on the beer. The problem cited in the thread is that the top of the barrel might dry out in this time - an issue that might be cured by laying a wet towel over the top of the barrel.
So, if there is active fermentation in the barrel, I think you're fine leaving it partially full, but for extended aging, you want it to be up to the top. The obvious danger of not filling the barrel is oxidation. In order to prevent this side effect, fill the barrel up.
When I filled my barrel, I did a double brew day on my system (20 gallons) and my buds had their three systems producing 10 gallons each. Filled the barrel in one day.