Hi there –
I don’t see an option to add a logo to the header
you can add a logo in Penscratch with the Jetpack plugin active – you’ll find the option in your Customizer’s Site Identity panel. Otherwise, you can download Penscratch 2 from the bottom of https://wordpress.com/theme/penscratch-2 and you’ll see a logo option without needing Jetpack.
my other issue is even though I deleted the menu below the heading, it still appears.
Like many themes, Penscratch displays a list of published pages by default if you haven’t added a custom menu.
If you’d like to remove the default menu, you can add some custom CSS:
.main-navigation {
display: none;
}
Don’t edit the theme files directly, otherwise your changes will be overwritten every time the theme is updated.
An easy way to add custom CSS is to use the CSS editor included in the Customizer as of WordPress 4.7. Head to Appearance > Customize > Additional CSS to add your custom CSS. Or add this to your child theme’s stylesheet, if you’re using a child theme.
If you need further help, could you provide a link to your site?