Hi,
Our recommendation is to use one Stuart account per store. You can find more information on this topic here - Account Creation Options.
In relation to using multiple web-hooks, There wouldn’t be a mixup between orders as each web-hook received would specific a unique order ID for the job, so even if you received multiple web-hooks at once for different stores for example, you’ll be able to easily identify which web-hook is for which store by the order ID sent with each web-hook.