You will only need one setup for the job you’re doing and from that setup you will add “operations”. Operations is what Fusion 360 refers to as a toolpath.
When you’re creating your setup you’ll choose a stock box point which is your zero origin. Every tool path “operation” listed under this setup will use that zero origin.
If you started the 1:50 min mark in this video it goes through making a setup and creating two operations in fusion 360.
The other method of adding an operation to a setup is right clicking on it and add operation is available in the drop-down list.