Sessions can be tricky, and the behavior varies by browser, server, and user actions.
I recommend trusting the cart's session management. As far as I know, there is only one session - although there may be many session variables.
What's really happening is that there is a file, usually stored in /tmp, with all the data for the session, which is read and updated as the user makes requests from and responds to the server. At the same time, there's a cookie on the client side, which stores the session id and perhaps some other data. The amount of time these files persist defines the length of the session.
When you work with open source software, the less you change, the better. Try to keep any modifications as simple as possible, and avoid modifying the original code - either fit into the architecture with modules, or use includes. It can be really difficult to avoid breaking the cart or adding security problems. If you feel like you need to make a lot of changes to use Magento, you might want to pick a different platform.