Multiple PCBs within one project
Related subject: Setting up a board as a Panel.
Within one project it is possible to divide a layout into several PCBs, see the following example: pic.t3001
You are able to maintain as much different layouts within one project as possible. You are restricted only by the maximum board size of 78.74 in² (=2.0 m²) over all.
See these two layouts within one project which you'd like to treat separately:

First prepare the layer structure:

The individual PCBs now need to be covered by filled rectangles being drawn on layer: "Separation into single PCBs". In our case it's layer no. 29:

The next step is to assign it a "PCB_AREA" and to give it a name (e. g. "PCB 1"). Doubleclick rectangle, press [Properties], type the property "PCB_AREA" to the list at the left and enter name of the single PCB right beside.

Both the Gerber export...

...and the generation of the Bill of Material allow choosing one of the PCBs:

.

