I think you’ve misunderstood how the GUI works.
When you replace a file in the GUI, it always gets a new media ID.
If you choose to update all instances, then the CMS simply visits all the layouts that media is used in and updates the link to the newly uploaded media ID.
The mcaas API call is not what you want at all. I think what you’d do is use the media edit route in the API, ensuring you pass the flag to update the media in all layouts:
http://xibo.org.uk/manual-tempel/api/#!/library/libraryEdit
I’m not certain of the exact mechanics of that. I’m sure @dan can add any further pointers if needed.
With regard to the file upload location, at a guess, you perhaps haven’t set a fully qualified path to the CMS library in the CMS settings. Ensure the path you entered is complete there.