Yes. You need one Simplify Commerce account for each project. That way you can have a different statement descriptor for each website. Statement descriptors help your customers keep everything straight when they see their transaction charges on their statements. They help you with your accounting because you can separate income by descriptor.
If you don't want to use another email address, there's an easy way to set up separate accounts. It's called Plus Addressing. Many email providers (such as Gmail) let you use a mailbox alias. If your current account is firstname.lastname@example.org, add a '+' followed by a descriptor to your second email address, such as email@example.com. Although emails will go to the same inbox, we will treat them as unique addresses.