The bank deposit is a separate process that you can get to by going to Transactions > Financial > Bank Deposits. Enter the date and your checkbook and all the items waiting to be deposited will show up in the scrolling list below. This allows you to group checks received together so that when you do your bank rec you see one number per total deposit, just as you do on the bank statement.
There is no way to automate this step, even if you get cash wired in or deposit one check at a time, you still have to post the bank deposit before it will show up in the checkbook and on the bank rec.
Hope that helps.