Hi Jakob,
You could also take a look at changing the image in the layout of your page, so for example in Atlas_Default. You could upload an image to the modeler and change the image in the layout manually. Hope that helps.
The logo can be set in custom_variables with
$brand-logo: "../../../logo.png";
$brand-logo-height: 50px;
$brand-logo-width: 40px;
I assume you did that? Are you sure the path is correct? Did you also compile the sass file? You can check with the developer console of your browser what is actually shown…
regarsd, Fabian