It seems like you’re actually asking three questions here; it’s likely your question will be put on hold because of this. Why do you need to add a custom post type?
If you’re interested in learning how to develop for WP you can skip the plugin for members and instead read the WP Codex entry on user roles and capabilities; this will let you limit who has access to the theme options pretty easily.
I had a quick peek at the theme files and it looks like it’s using the Options Framework to add its options. If you look inside options.php you’ll see that $options consists of a multi-dimensional array. The Options Framework is pretty easy to use; simply include the necessary files and then create your options as required.