I worked as Google ads strategist for 3 years almost. You can have as many websites you want under one account. If you use the same KWs for the 2 different websites, the system is going to show just one ad per account. But if you sell shoes on one website and on the second you sell flowers, for 2 different people, 2 different ads are going to show. One for who is searching shoes and one for who is searching flowers. Is clear enough?