Hey Kuba,
the primary menu in Sensei (black in the demo) is created using the native WordPress interface in “Appearance -> Menus” and then assigning the menu to the “Main Menu” location in the “Theme Locations” box on the same page. I am not sure I understood how you created the menu via custom HTML – could you please clarify a bit more and also provide a URL of your website if possible? Thanks!
Sincerely,
Andrew / Satori Studio