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:
Image 1: Two layouts in one project
By using the icon 
create a new layer having the function "Separation into single PCBs":
Image 2: Define a layer. Double click on a free layer line to open the dialog shown. From the drop down menu select the layer function.
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 #29. To do so, select the "Draw filled rectangles" tool in the drawing functions and click M2 on the number of the new layer in the layer stack in the sidebar on the right. This activates a layer to draw on. This is how you always do it in TARGET: Select the drawing tool and right-click on the layer number or on the color field of the layer in the layer stack on the right to activate it. Then draw.
Figure 2a: Use a filled rectangle upon layer 29
The next step is the important thing. Give each rectangle the property of a "PCB_AREA" and give it a name (e. g. "PCB 1"). Doubleclick one rectangle and press the [Properties] button in the dialog. In column "Property" type "PCB_AREA" to a free line. Enter an appropriate name of the single PCB right beside.
Figure 3: Doubleclick rectangle, press [Properties], enter name of single PCB at property "PCB_AREA"
Both the Gerber export...
Figure 4: XGerber and Excellon
...and the generation of the Bill of Material allow choosing one of the PCBs:
Figure 5: Select data set for the Bill of material (BoM)]]
.