This isn’t so much of a CCTM question as it is a question of how to use WP’s (somewhat primitive and wonky) menu registration functions. You can override the CCTM’s admin menu by implementing your own version of the menu configuration. See http://code.google.com/p/wordpress-custom-content-type-manager/wiki/Config_admin_menu
In addition, you can edit each content-type’s definition and reference a parent page where it should appear.
Was just a feature suggestion.
Gotcha: but I think you can already do this using the existing functionality. Due to how WP registers menu items, it’d be hard to automate this via a GUI. Just add the menu page in your post-type definition (see http://www.screencast.com/t/aw4iyvai)
bummer, the screencast link 404’s.
Actually, the screenshot should show the “Show In Menus” set to “Custom”…
Sorry for the 404… no idea what screencast is doing.
Just look in your post-type definition: there’s a field there specifically for the parent menu. See the docs for register_post_type() — it explains how that field is used.