You can customise the permalink for a custom post type, but it needs to
be hardcoded in the
rewrite parameter given to
register_post_type. You could use categories to achieve the
same thing though: set up a taxonomy for the first custom post type and
then use the posts to create a custom taxonomy for the second CPT (i.e. the
posts from the first CPT would become the categories for the second).
So you would add something like this pseudo-code to the edit page for
the second CPT:
- get all posts of type 'CPT1'
- loop through them to create a list of checkboxes
- display in a metabox
- save the result
There are still hoops to be jumped through to get those URLs going to
the right place, but it's a start.