If your account was set up properly, then reconciling (or balancing) your account should be pretty simple. It works similarly to balancing your checkbook. Click the "Reconcile" button at the bottom of the account register screen to begin. Enter the Ending Balance and Statement Ending Date as it appears on your bank statement, and click Continue. Next, check off each transaction that appears on your bank statement. When you've checked each transaction, the Cleared Balance should equal the Ending Balance from your statement, and the Difference should be zero.
When you click the finished button, you'll return to the account register screen. Each reconciled transaction will now have an "R" next to it indicating that it has been reconciled. If the transaction has a "c" next to it, that means you checked the transaction as having cleared the bank on the Reconcile screen, but haven't clicked finished to complete the reconciling process.
If the Reconcile box next to a transaction is empty, that transaction has not been checked or reconciled. If you realize a transaction is missing (such as a check entry or deposit) click on the "Return to Register" button. ChurchTrac will take you back to the account register screen. From there, go ahead and create the new transaction. When you are done click on Reconcile again, and you will be able to pick up where you left off in the reconcile process. The new transaction will now appear in the list of transactions for you to check off as cleared.