A General Journal typre entry (as opposed to a Cash Receipt or Cash Disbursement) will hit the balance in the GL without affecting the check register.  This is the approach to take if the check register can be reconciled to the bank statement using GL-J but does not agree with the GL balance for the account.  If you need to hit the check register in order to have GL-J and the bank statement agree, you need to use a CR or CD type transaction in GL-B which will hit both the chekc register and GL balance.