Im wondering if there is a way to change the default position of Wordpresses meta boxes such as "featured image" for custom post types without having to drag them manually?
You can remove the default meta boxes with remove_meta_box and re-add them in a different position with add_meta_box:
This will remove it from the side column and add it to the main column. change
I struggled with this too. I didn't really find a clean way to redefine the layout/order - particularly since it can be changed by the users when/if they drag the boxes.
I like to do things 'with' wordpress (it usually pays off), rathe than clash with it and the way wordpress does it is as follows:
wordpress stores the dragged positions per user per screen and there are a whole bunch of user-meta keys that it uses depending on which page/screen it is on.
So you could add a action or filter for each new user to set the user setting the way you want the default to be.
To get the idea of the user-meta metakeys you are looking for, see these screenshots: http://wpusersplugin.com/related-plugins/amr-user-templates/screenshots-for-user-templates/
(I ended up writing a generic plugin so that i could as admin define my preferred layout for all users for all sorts of pages/screens. Then they could alter that eg as they became more proficient. Also it won't break when wp changes things as me plugin just fetches the template user values, it doesn't even try to set the value to a hardcoded value.)