You can have as many carts as you want on a site. You could do separate checkout processes, or you could save a column in your cart to identify the tables to use. You could do it any number of ways it is just a matter of figuring out what database structure and user experience makes the most sense for your business.
If you wanted me to help, you could sign up for a premier support ticket and I'll review what you have and what you need and could help you design a new checkout to fit your needs.