Slightly confused by your question... but to change  the background  color of any image that is not using a transparent background, you need to open the image file in a graphics program and replace the background color. For example if you used Photoshop, you would select the foreground pixels (the people), inverse the selection and fill the selection with your new color.

I would suggest making a backup of the original image file before you make any edits.

I’m not sure if you’re asking one question (changing the background  color of a logo.gif) or two.In any case:To change  the logo  for a Portal go to Site Settings | General Settings | Change portal site properties…To change the background color  for a Portal go to the same place and add a custom  CSS stylesheetTo change the logo and colors for a WSS site use a custom theme

Let me articulate the problem  I am having a little better. I have
applied a Custom Theme through FrontPage. It looks good on all of
the pages  except for the display.aspx, create.aspx, viewlsts.aspx...
etc... (all admin pages)

I understand that the gif  is a transparent gif and you can modify
the color  but if you do that you are taking away the transparency of
the the gif file. This Gif would then be applied to every site that
has the transparent gif of logo.gif in the CSS (every site by
default)

One possible solution  is to replace the logo.gif with the blank.gif
and that work fine for the admin pages but then you lose some of the
spacing that the logo.gif provides. I suppose I could modify the CSS
to acheive the necessary spacing. Let me know if anyone else has
any other angles on this problem.

why not just use site definitions for the whole portal rather than frontpage?

Fastest fix is to open logo.gif, delete out all of the color  information
and save as a transparent GIF. You get the image off your pages  while
still retaining the spacing it provides in the layout.