The standard emails that Magento provide are good but you will probably need to make edits to them at some point when you're managing the site.
You can do this by going to System>Transactional Emails. Once there, click the Add New Template button in the top right hand corner. You are then presented with the New Email Template screen.
Select a template from the Template drop down menu and click Load Template and the HTML for that template will be displayed in the Template Content field.
Give the template a name by updating the Template Name field (preferably with a name that you can use to distinguish it from the Magento standard email templates whilst still being meaningful) and then edit the HTML in the Template Content field.
You can apply CSS styling to the email by updating the Template Styles field at the bottom of the page.
Once you're happy with your edits, save the template and go to System>Configuration and click the Sales Emails tab on the left hand side (under Sales).
In the main section you can select the email type that you wish to update (Order, Invoice etc.) and then select your new updated email template from the drop down list. In the case of the Order Email, this would be the New Order Confirmation Template drop down list.
Click Save and the new email template will be used in place of the Magento standard email template.