This file is surprising hard to find if you haven’t done it before…
Go into Content> Edit Templates> Select your template as usual.
Now for the oh so simple when you know it but damn frustrating when you don’t:
The files for the logo that appears on the shopping cart and checkout pages is not logo.png but logo_check.gif.
The easy was to change this image is to just redo the gif file and resave it under the same name. But you have more of a problem if you really want to use a different file format such as a png, you need to edit the actual head.tpl file.
The location for these pages is not with the normal customer/head.tpl. You need to go into Modules > and then select whatever checkout method you are using, either fast lane or one page checkout. Click in here and viola! There is the head.tpl file for those pages. You can edit the image path here. I usually change it to the same as what is used on the other pages, esp as they are all resized to the same size in the css file, and also fill in the alt tag while I am there.