1- Goto your main website after logged in.
2- Click on Customize and a new column will appear.
3- Click on Site Identity.
4- Click on Select logo.
5- Select your logo image.
6- You can crop your logo image or skip the cropping.
7- Click on Publish.
8- After that close the Customizer from the X button.

By default the logo image height is 50px, but if you want to increase that height for example to 60px.

1- Check the box if you want to modify the logo image settings.
2- Change Height value to 60.
3- Change Margin values to 10 for both values.

Another example if you want to increase the height to 70px.

The header Height is 80px so 80 – 70 = 10 and 10/2 = 5

1- Change Height value to 70.
2- Change Margin values to 5 for both values.

If you select the header layout 1 or 4 you will have the ability to set the header to transparent, and that require another logo for the transparent header, all you have to do is uploading your transparent header logo image and click on save changes.