You must be hand-writing the cheques?  Or is this a customer payment?  You have left out some information to give you a specifc answer but below is a general method to fix the issue.

Post a general journal entry to update the bank and the other account that should have been updated originally.  I would use the same date as the date you posted the cheque originally or the last day of the month you are trying to reconcile your bank statement.  Use the source to indicate it is a correction (I use Corr consistantly to indicate it is a correction entry), and the Comment to indicate the original journal entry that was wrong and to indicate why.