I have no experience with this other than looking around just now, but if you do what I just did (look around) you can probably figure out what to try. If you look at the Publish Settings, at the top there may be an option to choose a profile and perform other tasks related to them (based on my version of CS3).
One option involves exporting the profile. The profile is stored as an xml file, and if you export it somewhere convenient to find it, you can go thru it and see where it calls out the path to a default.html file. IF you open that default.html file you will likely see what you now see when you publish an html file in Flash.
So what you can probably do is create a new profile and adjust the profile to use a different html file... one which you edit to always have whatever you want it to always have. So when you want to use that profile you just select it. Or if you know that you will only ever use that, then you can either adjust your default profile to choose a different default html file... or just edit the default html file.
As I said, I have no experience, so it'll be up to you to try things and see (or wait for someone else to come along who has experience). Myself, I'd try things (with a new profile first).