The timing of the notifications works just like the regular Bit-Pay accounts.  You can choose to be notified immediately, after 1 confirmation, or after 6 confirmations.  But regardless of your notification setting, the accounting ledger is not updated until 6 confirmations.  Then each day we do a sweep and payout your accumulated balance by ACH direct deposit.  

The fees are 2.99% which includes the sell trade and the ACH, both of which cost us money to execute, but we do it all for the merchant.   They don't have to mess with anything, and they can spend their time running their business.