ACF automatically adds a meta box, so you shouldn’t need to add a custom meta box with your fields. Be sure to confirm the ‘Location’ settings on your ACF field group if it isn’t showing up. (You can also add multiple Field Groups if you want ACF fields to show up in different locations for the same post-type).
However, if you really need to manage ACF fields on your own, you can refer to their docs to obtain the field information via get_field_object and to manually update the field via update_field.
https://www.advancedcustomfields.com/resources/get_field_object/
https://www.advancedcustomfields.com/resources/update_field/