Let's say main monitor is A and second is B. B is connected to the primary slot of the graphic card and A to the secondary. Must do it this way due to adapter compatibility.

Problem is that even although I set A as primary and B as secondary in Gnome Settings, whenever I run an application the first time or send something to desktop, it goes to the B monitor instead of A.

Why? Is there any gsetting to force A as the primary monitor?

unfortunately, we're going to need a bt more information here

1) model of video card
2) proprietary driver?
3) distribution of linux used
4) what version of gnome
5) are you set at separate screens or one extended screen?
6) which monitor are you working with when you start, do you click an icon on screen2 and it appears on screen 1?

if possible, provide us with screen shots along with the information.

1) 01:00.0 VGA compatible controller: NVIDIA Corporation GM107 [GeForce GTX 750] (rev a2)
2) nvidia-driver: Installed: 340.65-2
3) Debian Jessie 8.2
4) 3.14.1
5) Extended screen.
6) When the PC is turned on, BIOS POST and Grub are seen on B (screen2) because it's attached to the first slot of the video card. Once the boot process gets to GDM, it switches to A (screen1) because that's what I choose in the options. So, when the PC is ready to be usable, the monitor I'm working with is A. Problem is that B is considered the main monitor for things like sending a file to desktop, or whenever I launch an application for the first time (i.e. first time I run an application after installation it shows up on B, then I move to A and close it. Next time I launch it, it will be on A).

For example, for this screenshot I chose to save it on desktop. The png file appeared on B (the left one) instead that on A which is the primary monitor.

Attached Thumbnails

 

ok, the most important part is here, you would make your adjustments in the nvidia-settings control panel, (run it as root, then save to the /etc/X11/xorg.conf, logout to apply the settings and you should be fine)

Noo, you didn't understand my problem

Gnome Settings, Nvidia and xrandr have the same configuration, right monitor is the primary and left monitor is the secondary. However, for some reason, the left monitor is taken as the default monitor for some actions, such as opening applications that haven't previously been opened or for new files created or sent to desktop via CLI (e.g. touch /home/user/Desktop/test), and I guess the reason is because the left monitor is connected to the primary slot of the graphic card (and can't connect it to the second because the DVI adapted won't work)

http://worth1000.s3.amazonaws.com/th...90572_60a9.jpg
this is my nvidia.conf for two heads, one monitor can be assigned as 'xs creen 0' and one as 'x screen 1'

at least in GUI, not sure about how to change which head is default at a lower level than that, other than to just physically swap the plugs and reverse which is which in the X config.