If I haven't lost you so far, we are in the home stretch now. This section is pretty confusiing so I suggest you also read the manpage for XF86Config, or at least skim it. Do it now... I'll wait.
root# > man XF86Config
Open your current XF86Config file and scroll down to the Monitor Section. You want to copy the following sections from the device specific XF86Config backup files you created above : Monitor, Device, Screen. These sections should go in your XF86Config file after the coresponding section in the file you have open. As you copy each section make certain that the Identifier is unique for each section, you will reference these Identifiers later.
Clear as Mud Right? You should now have a Monitor Section, a Device Section, and a Screen Section for EACH video card/monitor combination, each Section should have a unique Identifier. If you are still confused reread the prior paragraph. If that doesn't help, look at the sample XF86Config I have included at the end. You did read the manpage right?
Now you need to add the coresponding PCI BusID as an option at the end of each Device Section. The entry should look like this: BusID "PCI:0:12:0", substituting the three numbers with the PCI bus ID which identifies YOUR video card you should have this ID from the PCI Bus Section . Here is a sample Device Section for one of my video cards.
Section "Device" Identifier "FireGL" Driver "glint" BusID "PCI:1:0:0" EndSection
Please note, even AGP cards use this layout.
Now you need to edit the ServerLayout Section at the end of the XF86Config File. The ServerLayour Section is exactally that, it tells you what Screens to use, how to lay them out logically, and what input devices to assign to them. Your current layout is for one screen, keyboard, and mouse. For each Screen section you have created about you need reference in this section for them to appear in your display.
Using the existing screen reference as a starting point, create additional references for your other Screen Sections. The reference looks like this:
This defines the relationship between the "Screen 2" and "Screen 1". Valid Relationships include: RightOf, Below, Above, LeftOf, Absolute X Y, Relative. Use of the first four relationships is pretty obvious as illustrated in my sample:
Screen "Screen 2" Relationship "Screen 1"
Section "ServerLayout" Identifier "Simple Layout" Screen "Screen 2" Screen "Screen 1" RightOf "Screen 2" InputDevice "Mouse1" "CorePointer" InputDevice "Keyboard1" "CoreKeyboard" EndSection
I have other examples in the sample XF86Config section.