Themes FAQ and CSS FAQ are good starting points
However, to answer your question.
Files needed:
decaf/layout/frontpage.php and decaf/layout/general.php
PHP Code to look for:
(delete the part highlighted in red)
<h1 class="headermain"><?php echo $PAGE->heading ?></h1>
Add Logo place holder:
Add the following HTML code which is highlighted in blue.
<h1 class="headermain"><div id="logo"></div></h1>
You will need to make the same changes to both frontpage.php and general.php. That done the next stage is adding the CSS.
CSS File needed:
decaf/style/core.css
At the end of core.css file add the following CSS mark-up. (Be sure to use a text editor like Notepad as a word processor wont work.)
#logo {float: left; clear: both; width: 362px; height: 77px; position: relative; left: 50px; margin: 0; padding:0; background: url([[pix:theme|logo]]) left top no-repeat;}
Hopefully that should fix it. If you get stuck let me know.
Oh, nearly forgot! be sure there is a logo.png or logo.jpg or logo.gif (matters not what the file type is) in the pix folder of the decaf theme
Cheers
Mary
EDITED: I have just edited this today (12/8/2012) I found 2 typos where I put a colon : instead of a semi-colon ; in the CSS for the logo.
Please accept my apologies if you have had problems with this!