The PCB layout has the location of any physical element in that will appear in the assembled PCB and will describe the PCBA’s stack-up. Every component in a schematic has a corresponding entry in the PCB layout.
Altium will encode all PCB layout data in a single file, but other CAD tools may not. It will additionally automate synchronising files in the design process.
The usual design flow is to create an unpopulated board, then place components onto the board. At creation time, the layout file won’t have any components. We need to define the board size and shape and the stack-up (number of layers used, plane and signal layers).