if you are using them in html why dont you export them as separate images then reassemble in your layering fashion using div tags since those support the stacking you are after
<div id="Layer1" style="position:absolute; left:46px; top:24px; width:287px; height:181px; z-index:1"></div>
<div id="Layer1" style="position:absolute; left:46px; top:24px; width:287px; height:181px; z-index:2"></div>
would layer 2 images on top of each other. And you caould manipulatet them with JS. SOrry if I am not being a help. But I know what you are trying cannot be done in FW.
