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@Mohsin al Aulaqi

From what you described, applying a layer style will affect everything in the layer including unwanted white that was "knocked out" by the Multiply mode. The only way to apply a layer style on the logo itself is to first apply a mask to hide the white background as IamSam mentioned.

There's no other way around it, unless I'm missing something to your procedure or a procedure in the video you mention that you've forgotten before adding the layer style.....