In xorg terminology the video controller is called a device. Find your video controller with:

$ lspci | grep VGA
01:00.0 VGA compatible controller: ATI Technologies Inc Radeon R300 ND [Radeon 9700 Pro]

Add an identifier with this string to your /etc/X11/xorg.conf

Section "Device"
	Identifier	"ATI Technologies Inc Radeon R300 ND [Radeon 9700 Pro]"
	Busid		"PCI:1:0:0"
	Driver		"radeon"
	Vendorname	"ATI"
EndSection

Then in the Section “Monitor”, add the same 'foo' as identifier:

Section "Monitor"
   Identifier "foo"
   HorizSync 30.0 - 81.0
   VertRefresh 56.0 - 76.0
   Option "DPMS"
EndSection

In your Section “Screen” the monitor and device should be binded together. In this section also the allocation is made, which connector at the graphics card is referenced as screen 0 and which output is referenced as another screen in xorg terminology. Although for some this may seem obvious, screen 0 is not just the always first connector. Where should you start to count for screen 0 for example? And what if for some reason you want to overwrite the detected monitor types, or if a driver makes a false detection? The man-page about the radeon driver shows this vital information on this. In the following option:

Option "MonitorLayout" "string"

The possible monitor types are:
NONE – Not connected
CRT – Analog CRT monitor
TMDS – Desktop flat panel
LVDS – Laptop flat panel
This option can be used in following format:
Option “MonitorLayout” “[type on primary], [type on secondary]“
For example, Option “MonitorLayout” “CRT, TMDS”

Primary/Secondary head for dual-head cards:
(when only one port is used, it will be treated as the primary regardless)
Primary head:
DVI port on DVI+VGA cards
LCD output on laptops
Internal TMDS port on DVI+DVI cards
Secondary head:
VGA port on DVI+VGA cards
VGA port on laptops

External TMDS port on DVI+DVI cards

The default value is undefined.

Add the following line:

Section "Screen"
   ...
   Monitor "foo"
   ...
EndSection

In the current setup, the Edid-data which the VGA monitor supplies is incorrect, therefore X does not work instantaneously. A solution in this is to force it to ignore the Edid data. This can be done with:

....

The following xorg.conf file is my current file, which is not working fine yet. Graphic Controller: Ati Radeon 9700 Pro (R300 chipset), VGA output: Nec MultiSync LCD1830, DVI output: LaCie photon20vision. Default screen is Nec MultiSync LCD1830.

# xorg.conf (X.Org X Window System server configuration file)
#
# This file was generated by dexconf, the Debian X Configuration tool, using
# values from the debconf database.
#
# Edit this file with caution, and see the xorg.conf manual page.
# (Type "man xorg.conf" at the shell prompt.)
#
# This file is automatically updated on xserver-xorg package upgrades *only*
# if it has not been modified since the last upgrade of the xserver-xorg
# package.
#
# If you have edited this file but would like it to be automatically updated
# again, run the following command:
#   sudo dpkg-reconfigure -phigh xserver-xorg

Section "InputDevice"
	Identifier	"Generic Keyboard"
	Driver		"kbd"
	Option		"XkbRules"	"xorg"
	Option		"XkbModel"	"pc105"
	Option		"XkbLayout"	"us"
EndSection

Section "InputDevice"
	Identifier	"Configured Mouse"
	Driver		"mouse"
	Option		"CorePointer"
EndSection

Section "Device"
	Identifier	"ATI Technologies Inc Radeon R300 ND [Radeon 9700 Pro]"
	Busid		"PCI:1:0:0"
	Driver		"radeon"
	Vendorname	"ATI"
EndSection

Section "Monitor" 
        Identifier	"MultiSync LCD 1830"
        Vendorname	"NEC"
        Modelname	"NEC Multisync 1280x1024"
        Option		"DPMS"
        HorizSync       24-80
        VertRefresh     55-85
        modeline        "1280x1024_75" 135.0 1280 1296 1440 1688 1024 1025 1028 1066 +hsync +vsync
#       Gamma           1.0
EndSection

Section "Monitor"
	Identifier	"DVI-output"
	Vendorname	"LaCie"
	Modelname	"photon20vision 1600x1200"
	Option		"DPMS"
	HorizSync	31-75
	VertRefresh	56-85
	Modeline        "1600x1200_60"  160.96  1600 1704 1880 2160  1200 1201 1204 1242  +HSync +Vsync
EndSection

Section "Screen"
	Identifier	"Default Screen"
	Monitor		"MultiSync LCD 1830"
	Device		"ATI Technologies Inc Radeon R300 ND [Radeon 9700 Pro]"
   SubSection "Display"
         Depth 24
         Virtual 2880 1200
   EndSubSection
EndSection

Section "ServerLayout"
	Identifier	"Default Layout"
	Screen		"Default Screen"
EndSection

Add the xrandr command to the startup in the system preferences