WPtouch Pro's handling for custom post types can be activated via Settings > Site Compatibility > Custom Post Support. Simply check the "Enable custom post-type support" box and select the appropriate post types from the list that appears.
WPtouch Pro will store a profile of each custom post type selected, allowing them to be registered with WordPress for mobile visits. It will also attempt to register any taxonomies associated with those post types.
Enabling Include custom post-type posts in blog index will activate the custom post types in the main blog index (Posts page).
Note: Post types created by plugins do not need to and should not be selected.