when your trying to mix up flash with layers, it's important to remember to put your flash movie on it's own layer. That way you can decide its layered importance with the z-index setting.

A neat little trick I did was put the flash movie with a transparent wmode setting on it's own top layer. that way the movie opened up on top of the html in the background.
It's got me some kudos at my work.

you should have absolutely no problem manipulating the order of layers, regardless if it's flash or not.


hope that helps.