In the theme’s settings you can only enter hex values (#rrggbb). To apply rgba() you need to use custom styling:
element, #element_id, .element-class { background-color: rgba( red, green, blue, transparency ); }
For example:
body #pp-texttop { background-color: rgba(128, 128, 128, 0.5); }
to apply a 50% grey bg on the first text area. The other areas are:
body #front-columns-box – columns
body #pp-textmiddle – second text area
body #pp-textbottom – third text area
Posts and pages are more difficult to do this on.