I had a search around the forums, but couldn't find anything which documented this too clearly. So here's my contribution.
How do I include bank deposit details in the order confirmation email?
You need to create a custom notification template, and adjust it based on the payment method. We're using the bank deposit payment method (http://www.ubercart.org/contrib/2516), and if you aren't, you'll need to adjust the first line of the code below accordingly.
Notification templates are managed at Administer / Store administration / Configuration / Notification settings / Checkout.
The customer will receive an email as defined in the "Customer" notification here. The default notifications are stored in ubercart/uc_order/templates/ - "customer" is ubercart/uc_order/templates/customer.itpl.php
Duplicate this file to ubercart/uc_order/templates/my-customer.itpl.php - this made it appear as an option in the notification settings under "Customer checkout notification" as "my-customer"
Then add a block of code like this:
<?php if ( isset( $order->payment_method ) && $order->payment_method == 'bankdeposit' ) : ?>
<p>Please use the following details for a bank deposit (within YOUR COUNTRY HERE only)</p>
<p>Bank details are as follows:
<li>Bank: YOUR BANK HERE</li>
<li>Branch: YOUR BRANCH HERE</li>
<li>Account No. : YOUR BANK A/C HERE</li>
<p>When paying by bank deposit please make sure you have emailed orders@YOURSHOP.com the following information:</p>
<li>Reference used for the deposit: (name used on your invoice)</li>
<li>Date of deposit: (xx/xx/xx - the date you made the deposit)</li>
<li>Amount deposited: ($[order-total] - the amount you deposited)</li>
<li>Your order number: ([order-link] - the order number shown in this email)</li>
<li>Bank deposited from: (name of your bank)</li>
<?php endif ; ?>
Feel free to customise that, of course - the above is just what we used at http://www.notebookcity.co.nz/
Once that's done, make sure you've chosen "my-customer" for the customer notification, save your settings, and go test it with a bank deposit purchase.
Hope this helps!