In Flex Builder, you can just open the index.template.html
file in the html-template directory and replace it with the
template you want to use. As for mapping Apache dirs, you can set
the project up using Apache's virtual directories so that you
mirror your deployment structure.
But replacing the contents of the index.template.html only
works if I want to make another HTML, which I already did.
What I'm asking here is to be able to make a PHP template.
And the problem is not the structure of the Apache dirs, its
that when hitting the run button in Flex Builder, it will open a
local file, rather an URL of localhost.