Hi, Dave.
There’s two file systems you need to navigate – the Ubuntu instance on AWS is the first one, but OpenEMR runs in a container on that instance, it has its own full file system. You’ll need to get your logo onto the instance and then you’ll need to copy the file from the instance into the container (see docker cp) and then probably move it where it needs to go in the container.
The example command lines for docker exec discuss how to connect to the container to operate or explore within it.