This question has been answered by modxnewb. See the first response.
The link for the Logo would most likely be in an img tag in a Template (on the Elements tab in the Manager), though it could be in a TV or a chunk, in that case there would be a TV or chunk tag for it in the Template. If you want it to point another file, you can just change the reference there and save the Template, TV, or Chunk.
If you know the file and would just like to replace it, you can right-click on the folder its in on the Files tab and upload a file with the same name. You might want to back up the file first (by downloading it) if you don't already have a backup copy.