So, the problem I face is like this: I have a layer, which it will be placed on top of a pdf on the page. The PDF is either using to embed, or iframe to include it. Howeve
Generally you can get around these z-index issues by placing an iframe shim directly under the div. That is, it has the same size and location (but no actual content). I'm not 100% sure this works for PDFs, but I know this fixes some other z-index issues (such as select boxes on IE6).
iframe shims can be a pain if you're placing the div dynamically, since you have to move the iframe shim with it.