pdirect -
Customer Portal - one user name and password per QuickBooks customer. It is also pretty darn ugly, and built using the original design features available on the initial release of Method a couple years ago.
Contacts Portal - one user name and password per contact (since a QuickBooks customer can have many contacts on their account). It uses the latest design features available to Method and is a complete re-write.
If I had my way, we'd remove the Customer Portal from everyone's accounts - but we have no real way of knowing if they are actually in use still. All new accounts only have the Contacts Portal now. I recommend you go ahead and delete the Customer Portal if you know you aren't using it.
Here's a link to today's annoucement of the new Contacts Portal:
http://www.methodintegration.com/cs/blogs/methodblog/archive/2011/02/17/invoice-manager-for-quickbooks-online-portal.aspx
Paul