If you are using Skins*, you can't change your logo in the header or footer in your boilerplate or email draft. But you can change them in Skins.
Go to Skins (you find it under Content > Templates > Skins), if you want to change the logo for a specific project, choose the project, otherwise Account setting.
Click at Header (or Footer) at the Style tab to change the logo and or the size, link, alt text.
In the preview, you will see the changes immediately but if you have your email draft open while you do the changes, you need to reload the editor. If the logo isn't changing, double check if you made the changes in the right project or if you made the changes at Account settings, check the project. It might have it's own logo. In Skins, choose the project and check the logo settings. If you want to use the settings from Account settings, remove the project overwrites by clicking Reset. Don't fortget to save your changes.
If you are using a special header or footer, you might need to stick to a certain size of your logo. If you need to change the background color of your header/footer so it matches the logo, you can do it at this side-panel as well.
*Unsure if you are using a header or footer from Skins?
Click at Inspect at the header/footer block and unlock the block.
If you get a pop-up with the handlebar, you are using the header/footer from Skins.