In a cluster with more than 3 hosts, can you tell Fault Tolerance where to put the Fault Tolerance virtual machine or does it chose on its own?

You can place the original (or Primary virtual machine). You have full control with DRS or vMotion to assign it to any node. The placement of the Secondary, when created, is automatic based on the available hosts. But when the Secondary is created and placed, you can vMotion it to the preferred host.