I have been wondering how to do this for a while, and here is a fantastic post on this subject.

You need to do a couple of things… the first is this post:

it explains what you need to rename your file to for the flex builder to see what to do.

morearty.com/blog … First Post

and the second is this post… it explains how to change the run url, and debug url.

morearty.com/blog … Second Post