According to the Commerce 2 documentation, stores are optimized for two use cases:
We optimize for the two use cases:
One business that has one or more locations or 2. The marketplace
model (where you have sellers)
One or more locations This is the most common eCommerce situation where we have a single person, company, or organization that is taking
Marketplace model The marketplace model is where you have many sellers who are taking payment for unique products.
Each store can have a different currency, payment method, order flow, and so on. So, each store also has a separate, unique cart.
It seems there are two ways to do what you want.
Keep two different stores, one for B2B and one for B2C. If the configuration is mostly the same, you will have to duplicate a lot of config between the two stores. You will also need to keep the two stores separate so that B2B customers see the B2B store and B2C customers see the B2C store.
Just have one store. Add a select field to the products for admin to indicate whether it is a B2B product, B2C product, or both. Then, modify the views that show the products so that B2B customers see B2B products and B2C customers see B2C products. This way, you don't have to duplicate the config for the payment flow and so on.