You usually don't add a webpart to an aspx page template. You add the underlying control and any logic to the page. Webparts are specifically made to work with Portal and you will lose any ability to set properties via the UI if you add the webpart to the aspx page.
To specifically answer your question, you can simply add a reference to it on your aspx page just as you would with a regular ascx control and you'll have access to all the properties and the control in the code behind.