Have you enabled any payment gateway? The checkout process varies depending on the configured payment gateways, but there must be at least one enabled. For example if using only PayPal or google checkout then after logging in the user would see the buttons for those and would not have to fill out any customer information since that is sent back from from PayPal and Google whereas with Authorize.NET and WorldPay the customer information must be collected from the user on your site so a form will be showmn to collect it.
The user must be registered on the site for order to appear in their order history. When you entered the order in the back end did you look up the user and select him to create the order attached to the user?
Hope that helps,