On desktop screens, the Harmonic logo appears in one place: on the homepage’s Title panel, as you see here:

It looks like you’ve chosen to hide the Title section on your site, so that’s why you’re not seeing the logo.
I’ll have a look at your alignment issue separately.
The site title is hidden as it only display the text on the header, not the logo? I want my logo to appear on the header where the navigation is,