There are a few ways to do this;
If you are using the original skin, then all you need do is overwrite your new file to the directory which is /images/misc/vbulletin3_logo_white.gif , just make sure file is gif and your new image has the same name as above.
The alternative method is to edit the header, under templates and insert the image using HTML tags. To do so locate '<img src="$stylevar[titleimage]" border="0" alt="$vboptions[bbtitle]" ' in the main header template, and insert the image manually into the img src field, IE: replace the variable '$stylevar[titleimage]' with a file uploaded on a server.
I'm not sure why, but you failed to mention the appropriate way to do this.
AdminCP -> Styles and Templates -> Style Manager -> StyleVars -> Title Image -- Place the URL to the image here.
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To remove the whole logo section, remove this from the header template:
<!-- logo -->
<table border="0" width="$stylevar[outertablewidth]" cellpadding="0" cellspacing="0" align="center">
<tr>
<td align="$stylevar[left]" class="logobg"><a href="$vboptions[forumhome].php$session[sessionurl_q]"><div align="center"><img src="$stylevar[titleimage]" border="0" alt="$vboptions[bbtitle]" /></div></a></td>
</tr>
</table>
<!-- /logo -->
That should do it.