just wanted to say how I solved exactly the same problem:
1. To fix the widget sidebar on the bottom problem: If you already uploaded the new logo using Appearance-> Mystique settings and after clicking on save the old logo reappeared and your sidebar with widgets moved to the bottom, then just go again to Mystique settings and click on "Remove" under the header image. This will fix the sidebar problem and return it back on the side. You might need to select again the Layout Style (Global).
Don't be afraid, your old logo will still be there. I believe somehow the new logo is still uploaded although not visible, which messes with the widths and so the sidebar.
2. To change the logo image, this worked for me:
Find where is your logo located. You can right click on the logo of your blog and select "copy link location". If you paste it anywhere in the text editor, it shall look like this (I have mystique-child theme)
Go to your cpanel and via ftp go into the directory where your logo image is stored.
Delete this image.
Give the very same file name to the new logo image (MyLogoImage.png)
Upload it to the directory where the old logo was.
Now - to see instantly all the changes, I recommend to install plugin "Clear Cache For Me" and on the Dashboard just after you made your changes, click on the "Clear Cache Now!" button.
Then simply reload your blog in the browser and enjoy.
Hope this helps!