Hi,
3. For what I read about your process, it is not linked with "multiple cart" system.
If you add some products while not being logged, the cart will be link to the user session.
For the cart when the user is logged, the link will be done on the user id.
So, for HikaShop, it is two different carts for two different "accounts", even if it's the same person.
5. Thanks for the website link.
The checkout SEF name allow HikaShop to understand when the checkout is "called" ; but if you use the option "force menu on checkout", you can have an a fixed menu for the checkout (and choose the url which will be used).
So the best for you will be to create a specific menu for the checkout and assign it in the HikaShop configuration.
Regards,