I have purposely kept the output of phpPortfolio as vanilla as possible to facilitate working the portfolio into your existing site. All output is valid xhtml 1.0 transitional.
The simplest way to customize your portfolio is to edit the head.php and foot.php files to suit your site's design. Alternately, you can just change the calls to head.php and foot.php in the index.php file to point to your existing site's common header and footer, if you are using such a structure. Of course, if you do this you will lose the menu. Refer to the provided menu.php for examples of how to build the required links for phpPortfolio into your existing menu system.
Note: it is important to include the line$user_level = $_SESSION['user_level']; somewhere near the top of your menu, if you are building your own menu file!
Another simple way to effect dramatic changes to the look and feel of your portfolio is to poke around in the portfolio.css file. You should look in there even if you are dropping phpPortfolio into an existing layout, as there are a number of classes you may want to include in your existing global stylesheet. None of these classes are essential for phpPortfolio to render, but they do offer control to you over a number of internal items that will otherwise inherit whatever properties they can from your existing stylesheet.
It is also fairly simple (if you are using your own header and footer) to move index.php out of the portfolio directory (re-naming it something else, like portfolio.php) and simplify your site's directory structure. For example...
By default, your site's directory structure might look something like this...
/domain.com/ index.php page2.php portfolio/ foot.php head.php index.php menu.php portfolio_app/ assorted files and directories here portfolio.css style.css
You could simplify that to be something like this...
/domain.com/ index.php page2.php portfolio_app/ assorted files and directories here portfolio.php style.css