Mmmm. This might not be the right solution for you, but it might put you on the right track.
Check out my own forums -
http://flare.solareclipse.net/ Note how there's a big logo in the upper left, but BBTitle isn't there. Well, BBTitle doesn't SEEM to be there - in order to push the board down enough, I actually made BBTitle a large transparent gif.
The logo in the upper left is positioned there using CSS, and floated above the rest of the contents. (In the old school methods, this would have been done using a set of tables and perfectly sliced images in the cells.)
This works perfectly for me, as I know that my upper left side of the board will always be perfectly positioned. That MIGHT not be the case for you... and as you seem to want to get rid of the logo entirely.
If you want to just push down the contents of the entire board, for all pages, that's pretty easy.
Edit public_common, search for "standard_title_table" - there will be two instances, both being variables that hold the entire upper table. The first one is for all pages, the second is for search pages (the search pages have their own logo for some reason lost to time). Just stick some sort of spacer there - something like:
<div style="height: 100px;"> </div>
... where 100px is how many pixels you wish to shift things.
Do note that pushing the board contents down too far can make it hard for users on lower resolutions (~20% still use 800x600!) to navigate the board easily.