There are two ways to use ConvertKit with multiple websites.
The first, and easiest, is to have multiple ConvertKit accounts, as everything can live in its own account and you don't have to worry about accidentally crossing the streams :) The downside here is that you have to maintain (and possibly pay for) multiple accounts.
The other option is to use a single ConvertKit account, but be diligent about ensuring all subscribers get tagged/segmented to identify where they came from. You'll then need to ensure that each Broadcast and Sequence only goes to the appropriate audience. You can setup multiple "From" email addresses, and use completely different email templates if you'd like. While this allows you to use a single account and potentially save some money, it requires a lot more manual work on your part to keep everything separate, while it's really mixed all together...