I'm building a mobile phone version of my work's website by creating a custom theme, which is activated by a custom plugin whenever an iPhone/iPad/iPod browses the site. The trouble I'm having right now is that the theme, a premium theme called Across, uses custom post types to create a Portfolio. This changes the permalink structure of the site, and generally makes things complicated.
Right now my theme is changed by the plugin hook template_redirect, but I can't seem to figure out how to use the other theme's custom post structure. What can I do?