Yes I struggled with this at first too. But it does work
When creating your tables make sure you add the Wizards for Joomla Access. For completeness I also routinely add the wizards for Created by and Modified By, checkin/checkout, creation date etc. These are all Joomla standard fields and it makes sense to have them.
With all of this in your tables then your views should limit based n the ACL settings you set in Joomla. ie: Load your component, go to your component in backend, and amend Options to allow user groups to view and edit their own only. (ps: I have not seen where I can set permissions directly in J-Cook Builder)
PS: One gotcha I have found is that if you create a fly view, which has no fields or tool bar (a blank canvas which you create the fields yourself) then obviosuly you will have to add your own code to limit the that view via the ACL