You have 2 choice.
The first is that you create your options pages as sub pages of the CPT. This is done by using acf_add_options_sub_page() and setting the parent slug to the URL of your CPT.
The second option is to set up the CPT under the top level options page. If you do this you will loose links to the standard CPT sub menus (all, add new, etc) and these will only be available from the main CPT admin list page. I have instructions for doing this here https://github.com/Hube2/acf-filters-and-functions/blob/master/acf-options-page-w-cpt-children.php
