Hello Theo,
thanks for choosing Bento! The “logo on the left, in line with the menu” is the default setting for the header layout in the theme, so make sure the “Menu Layout” option in the “Site Layout” tab of the “Appearance – Customize” admin section is set to the default value. If it already is, and the logo still appears above the menu, please provide the URL of your web page, I’ll need to see the live code to give a more precise recommendation. Thank you!