OK - So you've created this awesome layout in Photoshop but the only version of the logo you have has a white background and you want one with no background... here's how you can do it.
Place the logo into your layout and with it selected open the Layer Style dialog.
In the 'Blend If' area click on the white triangle on the top slider and move it to the centre. This will start to make the white portion of the logo transparent. You may need to split the triangle in half to refine the transparency more - to do this press the Option/Alt key and click on the triangle and it will split in half. You can now adjust the transparency by moving the 2 halves of the triangle till it looks best.
Technically the white box is still there and you'll see it if you add any other layer styles to the logo. You can get around this by doing the following steps:
Click on 'Create a New Layer' icon to add a new layer.
Select both the logo layer and the new blank layer and press Command-E/Ctrl-E to merge the logo layer and the new blank layer. Now any style you apply to the logo will appear around the shape of your logo rather than the square box.