Hi,
Are you talking about the "Add a 'become a partner' checkbox on the registration form" setting ? If you activate that setting, you'll get a checkbox on the HikaShop registration form so that the user can check it to become a partner.
HikaShop won't add that checkbox to the Joomla registration form, and thus the users registering from there won't be able to do so.
What you can do is to activate the "Redirect Joomla registration to HikaShop Plugin" in the Joomla plugins manager. That way, your users will only register through HikaShop, and thus they will get the checkbox.