This is a great question. You can use the same feed to upload the products what will be important is to create two separate collections for them you can use their unique identifiers to categorize them into individual collections. Once you have done this you can configure different criteria each criteria can use a different collection. You can read more about collections here: Collections I hope this helps you.
Mihnea Docea | Technical Support Rep, Customer Care | Customer & Employee Experience | Adobe | (:: 1 (800) 497-0335