The portfolio works off the blog concept of WordPress, so right now your order of portfolio items (posts) will be by date.
There are plugins that help people do custom ordering of posts which you might want to check out. As to any specific ones, I’ve never used any myself, so I won’t be able to suggest any. The other method which is not a fun one really is to change the date of each portfolio item to the order you want.
It’s not the most flexible portfolio method but it’s one I did without the use of custom post scripts and.or plugins. It also makes it easier to change themes without too much layout disruption.
Another method would be to create a portfolio manually in a page….which I will be writing a tutorial for after I launch my new version of Styled Themes shortly. The manual method I prefer overall because it gives the most flexibility and a person can create their own layout to fit their type of portfolio content.