This is how I use option GL-J, not necessarily the TRUE instructions for this module.
 
The Cash Receipts and Cash Disbursements journal transactions feed info to the Check Register.  So you must be using these journals to capture deposits and disbursements.
 
First, you must enter a beginning cash balance via AD-B, which assumes you have established cash accounts,  If not, you can enter a new cash account in AD-B.
 
Once transactions have been processed in the cash receipts and cash disbursements journals to the provided cash account(s), select GL-J, Reconcile Check Register.
 
Select the cash account you wish to reconcile,  
Then select reconcile to bank statement,
and enter a time frame for recconciliation.
 
For example, if I am reconciling for the month of December, I will select those deposits and disbursements with 00/00/00 beginning date and ending date of 12/31.  This will allow for any uncleared checks processed before December, and any deposits made in November or prior that were deposits in transit as far as the bank was concerned.
 
I then tag the deposit details to the deposits listed on the bank statement.  I make sure the total of deposits selected in GL-J  agrees with the total deposits on the bank statement.
 
Then I tag the cleared checks, wires and other disbursements, ensuring the total also matches that on the bank statement.
 
Anything remaining should be uncleared checks and deposits in transit.  This number is the difference between the Bank's cash balance per statement and my company book's cash balance at 12/31. However, this assumes that last month was recconiled properly.  
 
GL-I, Print Check Register, will print listings of uncleared checks and deposits, so you have the details to the difference.  
 
HOPE this provides a little insight.
 
Linda

Quote from lmk223a on 01/28/08 at 07:15:31:

 
Note that if you had NSF checks or Reversed Payments, or Voided Checks, you will have to wait to tag them until after you make sure the Total Deposits and Total Checks agrees with your statement as there will be extra Cr and Dr in there. The Net may come out right but you won't be able to compare the Statement Totals with the GL-J Totals.