I assume you mean you want to deploy the PDF along with the Java Web Start application? If so, you simply need to package the PDF(s) with your webstart application. When your application downloads and runs, the PDFs will have come too, and your code can use the getClass().getResource("/where/is/my.pdf") type of lookup to locate the PDF and then operate on it for display. You might also need to get your code to read the PDF out of the resources and save it in a temp file (File.createTempFile()) so that the PDF viewer can see it.
rough idea:
// Find the PDF in the Webstart App download
InputStream in = getClass().getResourceAsStream("/where/is/my.pdf");
// create a temp file to copy the pdf to
File tmpFile = File.createTempFile("my", "pdf");
OutputStream out = new FileOutputStream(tmpFile);
// stream the file from in to out ... heaps of examples on the net for doing this ("copy files")
// display the file
Desktop.getDesktop().open(tmpFile);
// ideally clean the tmp file up at some point.