It pretty much has to be seperate.
A lot of people have to do this merely for search engine reasons (that
is, dynamic content using # isnt well handeled by crawlers - assuming
they handel javascript at all, which most dont).
The typical way is to make a basic PHP based site which GWT provides a
shiny alternative view too.
While I dont know precisely what you need, you could (for example)
have the PHP take data from MySQL and echo it out formated beween
<NOSCRIPT> tags, but also have the data avaliable for the javascript
by echoing it to javacript var.
Either way, its a pain.