Rightclick on the original and save it to your desktop. Open the saved graphic and paint it whatever solid background color or pattern you want. Paste your logo on top (may have to resize the logo to fit). Merge layers if necessary. Touch up if necessary. Save the file.
Right click on the orginal logo (on the web) again and choose properties to find out where it's located. FTP or somehow upload your updated file to that location, choosing "overwrite" if you're asked.
By pasting your logo on top of the old one you make it easy to get the correct size. This is a quick way to break in a new theme. You can often use some of the colors on the original theme logo to help your graphic blend with the theme.
Brian