Uhhh... maybe a specific example will help. Lets say you start with accounts/balances of:
A: 5
B: 5
"": 1
Total wallet balance: 11
Now you send 5 BTC from A, and pay a 0.01BTC fee. Account balances will be:
A: -0.01 BTC
B: 5
"": 1
Total wallet balance: 5.99
The fee isn't 'taken' from either B or "". You'll have to decide how to handle fees; for ClearCoin, I keep a positive balance in the "" account and automatically move coins from there if a transaction results in a fee (so for the above case, 0.01 bitcoins would be moved from the "" account to A, so A ended up with a zero balance and the fee is paid from "").