By default, the plots listed in the CAM/Plot dialog are for a single layer. However, it is quite easy to generate a plot that combines multiple layers, which is quite useful for things like assembly documentation.
To do this, first create or choose the plot for the first layer to appear on your combined plot, just as if you were outputting that layer on its own. With the row for this plot selected in the list of plots, click the button Add to Plot at the right-hand side of the dialog.
This brings up the Plot Wizard, the same one as you would see when creating a normal plot. The difference here though is that if you click Next, you will see that the Name and other parameters on that page are greyed out. This shows you that you are adding an extra 'sub plot' to that named plot.
Click Next again, and now choose the layer you want to add into the plot. If your original plot was the Top Assembly layer for example, you may want to add your Documentation layer. Continue through the Wizard (note that there are options here to position the additional plot relative to the main one), and when you return to the main CAM/Plot dialog you will see an extra row underneath the main one, but with the first few cells of the grid greyed out to show it is a subsidiary row.
Now when you generate that plot, you will get both the layers at once on the same output, be it PDF, Gerber or whatever output device you have chosen. You can continue adding subsidiary plots, there is no limit to how many you can combine.