So what is the proper way to store the Phantom for more than a week without the batteries dying? with a 20% charge or a 100% ?

I have two batteries giving me this ugly message!

"Damaged Cell Warning, not recomend to flight"

hmmm sounds like you have a bad cell in your lipo (battery) not sure though as i do not own a phanton yet but i do use alot of lipos for my rc cars can you check the voltage in each cell?

The newer batteries will auto discharge after 10 days as a protection.   Best to store between 20 and 40%. BUT,... if you're getting a damaged cell warning, I wouldn't trust using them.  How old are they?

If they are newer batteries, I would contact your dealer or DJI.  

Definitely do not store those with your Phantom at all at this point!
40-50% charge is o.k. though the newer batteries have an auto discharge feature that even if fully charged should auto discharge, either way I would never store something that size fully charged in a closed case for any extended period...just my .02..
Check with your warranty/dealer/DJI as Tahoe Ed suggests.