Thought this might be of some use to some.
I’m working on an as project in Flex Builder, into which I needed to pass variables from SWFObject. Whilst it’s easy enough to overwrite the generated html in the bin folder, it is a bit of a pain, cos that way you lose the debugging/tracing etc.
So, what I discovered is that there is a file called index.template.html in the html-template folder, which is used to generate the html page. Replace this file with a slightly modified SWFObject template, chuck swfobject.js into your html-template folder (and probably the bin folder for good measure) and Bob’s your uncle 
[update] The previous template was based on the static embed – this meant you couldn’t actually add params!
Dynamic SWFObject template