Since you have already posted entries against to your GL Account for your bank, it will not match your actual bank balance if you are using the bank rec, you would have reverse those entries.

From now you would have to enter all deposits as deposits in the bank services bank reconciliation and choose the correct GL Account. Journal Entries to the GL Account made through GL will are not recognized by the bank services module and therefore don't affect the bank services "sub-ledger".

Hope that is clear.