First, make sure you have set up a Login Welcome Page (LWP) and a Membership Options Page (MOP) in
Then let's say that your custom post type is called
book. Now go to
Restriction Options -> Post Access Restrictions and type
all-book in the box for the relevant level. Then scroll to then end of the page and hit
Save All Changes.
This will ensure that only those with access to this level will be able to access the
book custom post type (CPT) on the front-end.
Note, though, that s2Member doesn't regulate admin page access in the same way. It's just either on or off; s2Member cannot regulate who gets to see the
book CPT from the admin pages.
If you want to regulate who can create such CPTs, you will either need custom code, or another plugin, or else you could force them to create such CPTs from the front-end by using an appropriate form.