Changes to Portfolio Press themes that will survive updates

I am working on a client’s site on localhost using Portfolio Press. I want the functionality of the portfolio page but also want to change the appearance and some behavior to match the client’s fonts and branding. I have made changes to the CSS, the jquery, several theme files, including the header.php, content-portfolio.php, footer.php, among others.

How can I leave the theme open to future updates while preserving my changes? My current method is to keep copies of my changed files in a “safe” folder so my formatting can be restored.

Mark

http://wordpress.org/extend/themes/portfolio-press/