What's the problem that you have got by using the html wrapper file generated in FlexBuilder..
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If you have a pre-existing html file that you need to use you can always use its structure as your template(adjusted to suit the insertion of the support scripts that really should be used with the swf). When you build your project you will have the html file as per your project requirements.
I just wanted to make sure the best practice to embed my flex file, it seems like modifying the flex generated html is the best way.
Thanks a lot! I think both of you provided the correct answer. I will give
BhaskerChari correct answer since he is the first one replying me. Helpful answer for you too David. Thanks again!