In XSLT 2.0 you can generate multiple output documents using the xsl:result-document instruction.
Some XSLT 1.0 processors have vendor extensions which do the same thing.
If you haven't got access to this capability (i.e. you're using a standard XSLT 1.0 processor) then you need to call the transformer once per output file from your application layer, passing a parameter to say which output file you want to generate.
Michael Kay
http://www.saxonica.com/
Author, XSLT Programmer's Reference and XPath 2.0 Programmer's Reference