Make a file some-name.sh. PLace your script inside. Example:

#!/bin/bash

setxkbmap -option '' 'us,bg' ',phonetic' 'grp:alt_shift_toggle,grp_led:scroll'

Save it and and type in terminal: chmod +x /path-to-directory/some-name.sh to make it executable
Path-to-directory is the directory where you stored your file and some-name.sh is the name of your file. Name it any way you want. To run it at startup follow my previous message.
setxkbmap sets the keyboard map in X - you can choose your languages where 'us,bg' is phonetic is my cyrillic keyboard layout. Notice the COMA before it. It tells to setxkbmap that it applies to the second option - in my case BG. And the last section is for the keyboard switcher. I chose Alt+Shift to toggle between keyboard layouts