Hi there Paul!
It has been a long time since I set up my site but I am pretty sure I ran the checkout wizard on the shopping cart page and it then created all the other pages for the checkout process automatically.
As Eric just noted in the post above the store cart summary behavior would be added on the confirm page.
The Universal email would be added on the pages where you want the email to trigger. In my case it was the confirm page just before the checkout_success page. That way the email receipt goes out as the order and payment are being processed.
As for security assist....I have no idea as I don't use that extension. You may want to start a new topic in the "security assist" section.
These exentsions seem a bit tough to use at first but once you begin to understand the process you'll really apreciate how versitile they really are.