Hey @Pawel_Kosiorek,
glad you like my theme! 
You only showed the html code and I guess the CSS is right. But did you apply the JS also in the head?
This code here:
https://github.com/B-iggy/discourse-dark-theme/blob/master/alien-night-theme--theme-switcher.js
Needs to be put in the section (Common).
The HTML goes to the “After Header” for Desktop and Mobile independently since they are a bit different.