A little late, but it may help someone else.
If you know how to use the code inspector tool in your browser, you can use it to see what dimensions Shopify is currently rendering your logo at. Once you know those numbers, simply double both the width and height. That would be the dimensions of the logo you want to use.
For example, Shopify was rendering my logo at 425px by 40px so I exported my logo at 850px x 80px, which was the version I used as my checkout page logo. Hope this helps.