I'm a new QBO user following along, as I'm having the same problem.  For those not familiar, BofA uses a parent account (no card) that the sub accounts (each of the physical cards) feed into.  When downloading transactions, the parent account only show credits and the sub accounts only show debits.  I've reconciled the credit card account, however the bank balance and the QBO balances don't match.

I show a huge negative balance for the card account and a huge positive balance for the parent account, as the debits and credits don't seem to cross accounts in QBO like they do on the BofA side.

I've tried nesting these differently in the chart of accounts, but can't seem to find a way to make this work like I believe it should.  Hoping someone can help.