The most basic way is to set your background to transparent, in your menu option, “File/Publish settings”. Click on the html tab and mark off that checkbox.
The resulting published html page can be opened with your favorite html editor.
From there, just look at the place where it says something like “window=transparent”. If you memorize the way that this html is writen, you can just go in and edit the object and embed tags from any script that you make. (Note:there are two locations in the html where it set’s transparency… you have to set them both.)