I have read this
http://msdn.microsoft.com/en-us/library/bb251011.aspx
which tells you how to get and xslt to not be overwritten.
I know the basics of xslt, but haven't used it in years. I find plenty of references to - "create the xslt file in word" however I can't find anywhere that it says exactly the format, what the relevant tags in infopath are etc.
I know someone here is bound to have done it and can probably offer a few links to tutorials.