Reconcilliation should be a simple procedure, simply clicking the reconcile button for each credit and debit. In real life, however, we have to "postpone" and "edit" transactions as we find problems. In my case, I reconcile the deposits first as it's a smaller number of transactions, then the witdrawals.
It's more difficult than it should be to determine when the deposits and the withdrawals are both accurate, but this is necessary in order to determine whether any error is in the deposits or withdrawals.
In my case, on the Reconcile tab, I show "Unreconciled," then "Deposits." Unfortunely, there is no dollar total for the displayed values - it shows only the difference between the beginning and ending balances for the bank's month, a useless figure at this point. As I click the deposits, this difference changes; when I'm complete, I manually add or subtract the new difference to the old difference to determine the amount of deposits for the month. Then I compare that figure to the bank's Deposits amount. Having to do that is absurd for a figure that could be calculated quickly by a computer.
I recommend you display the total amounts of any sort or display commanded, both in Checkbook and in Reconcile. How much did I deposit this month? How much did I write checks for? That would be a useful feature.