Solved.
OK, there are 2 ways. First is the script that greps layout from 'setxkbmap -v' and second(one I was looking for) - edit
/etc/X11/xorg.conf (or
/etc/X11/XF86Config-4) :
Code:
Section "InputDevice"
# ...
Option "XkbLayout" "us,cz_qwerty"
Option "XkbOptions" "grp:alt_shift_toggle,grp_led:scroll"
EndSection