first you need to understand the support parameter, so from the codex:
Register support of certain features for a given post type(s). All
features are directly associated with a functional area of the edit
screen, such as the editor or a meta box. Additionally, the
‘revisions’ feature dictates whether the post type will store
revisions, and the ‘comments’ feature dictates whether the comments
count will show on the edit screen.
So basically what this means is that if you register your post type with custom-fields in the support parameter of register_post_type eg:
'supports' => array('custom-fields','title','editor','author','thumbnail','excerpt','comments')
your post type will support custom fields and the custom fields metabox will show on your custom post type edit screen, this one: 
and how to use them is another question which has a great entry in the codex