GD doesn't support GIF anymore, so getting a transparent image won't be possible i don't believe. option maybe to not have it transparent?
could use CSS positioning w/ transparent GIF for your logo:
<div id="Layer1" z-index:1;>
<img src="main.jpg">
</div>
<div id="Layer2" style="position:relative; z-index:2; left: 125px; top: -75px">
<img src="logo.gif">
</div>
there's a way to make the logo relative to the main image you want to overlay it w/ not exactly sure the method, but can toy w/ the above code.
OR, could forgo transparency and use a square? logo? over your image, and then figure out how to overlay those two w/ GD, that i'm not sure of.
may want to look at the following link too, it has something w/ transparent in it for GD, i've not checked it out much:
http://db.org/demo/gd/scale-and-overlay.php/source