You can have more than one PCB in the PCB View - just drag another 'Rectangular PCB - Resizable' from Core Parts on to the PCB view. Then you can put each of your components on whichever of the PCBs you want it to be on. If you don't want to leave unrouted nets you'll have to add headers for the connections you want to make between PCBs and join them with jumpers, I guess.
If you want to export only a part of your design, save it under a new name and delete the bits you don't want in the export.