What you need to do is to make custom user meta fields.
Links these metafields to a custom category linked to your custom post type.
Use this code for a checkbox feeling:
<input type="checkbox" id="category-<?php echo $post_type->term_id ?>" <?php if($user_cats[0] && in_array( $post_type->term_id, $user_cats[0] )) echo 'checked=checked';?>
name="categories[]" value="<?php echo $post_type->term_id;?>"/>
Every custom category you make in the custom post type will be linked to the users profile. this way you can assign posts to a certain user.