All possible and provided for by using WebStart.
Have a look at this:
http://androgynous-guild.com/jUniUploader.jnlp
If you click the link, it will start jUniUploader with the default URL for UniAdmin set to the UniAdmin of Androgynous.
That way, people that start the program for the first time will have all their settings configured fully automatically.
If you download the JNLP file and change this in it:
property name="uniadmin" value="http://androgynous-guild.com/roster/uniadmin/interface.php" />
to reflect your own UniAdmin URL, you can just upload the odified JNLP file to your guild's website and link to that one. It will automatically configure your guildies' jUniUploader from your own UniAdmin.
I hope I understood you correctly when you spoke of "embedding". Just to clearify, Java WebStart is
not Java Applets. It's far more advanced than that. As such, the application (jUniUploader) isn't really embedded in the webpage, it's just automatically downloaded and configured by your webpage, and kept up to date whenever your people click the link. No installation or configuration needed, just a click. From that point on, jUniUploader saves its configuration on your guildies' computer for the next time they start jUniUploader.