Welcome to the forum, Tim!
You are at the very beginning of a long learning curve. Short answer -- yes you have missed a few things. Too many to summarize here IMO.
A good place to start would be your owner's manual, and the following Battery School, for general info about caring for your batteries:
http://www.batteriesnorthwest.com/ba...hool.cfm?TID=0
Yes, there are loads running in the background, like the propane detector.
The new search function in the blue box above works great, and these results would be another good place for more info:
"phantom battery loads" --
https://www.google.com/search?q=phan...=airforums.com
Also the various topics in the Batteries etc. sub-forum will help:
http://www.airforums.com/forums/f449/
Lots of information to absorb . . .
We generally are able to store our 2014 FC20 for 7-10 days, without charging the batteries, with the batteries in "Store" mode. After this time, the battery voltage drops below 12.5 [90%], and it is time to charge again. If they go below ~12.3 volts [~50%], then more pronounced damage starts to occur.
Good luck,
Peter
PS -- FYI you have probably damaged your batteries somewhat by letting them go dead. What to do when you have charged them again is another long discussion -- for another time IMO.