Adding a custom printer to Cura
Your manual is in another Castle!
The manual you look at is for Cura (1) 15.04. You are however using Ultimaker Cura 3, most likely the most recent 3.6.
Quick references
The machine setup is for the physical settings of the machine - build volume, nozzle diameter, coordinate system and such.
The other settings you refer to are all set in the right bar, but you will have to switch from simple to advanced mode, and possibly activate the settings you need.