When using the portfolio shortcode, you can specify how they are ordered (see the Portfolio shortcode page). By default they are ordered by menu_order which means you can manually specify the ordering when editing the portfolio item. To set the menu_order, when editing or adding a portfolio item you will see a box on the right-hand side named Attributes.
Enter a number in the box under Order. This field will then be used to order the portfolio items when they are set to order by menu_order.