You could just ask the person who admins the university server to set up a virtual web site for your stuff, but that would require that you move all your web stuff to the university server and run it from there. I'm not sure what you mean by "embedded webserver." Embedded in what? A timex watch? A rock? I'll assume you mean you need to or want to leave the server where it is and have people access it directly from the Internet.
There's a few ways to do this. One would be to put the embedded webserver directly on the Internet. That is, give it a publicly addressable IP address. (e.g., 211.32.55.121) It would then be a peer of the university's web server. You would register that IP address in your university's DNS servers so the outside world could find it by name. The university's web server would be at
http://www.myuniversity.edu and yours would be at something like
http://ourcoolsite.myuniversity.edu. You could even add a second Ethernet card in that box so that Internet requests come to one card from the firewall and inside requests come to the other Ethernet card. (Easy to do with Linux. Can't say for windows.)
You could also talk with the people who administer your firewall/proxy server and set up a port-forward from Internet requests to
http://anothercoolsite.myuniversity.edu to the embedded web server on the internal LAN. You would still register the name with your school's DNS servers, but when the firewall see's an Internet request to the embedded web server, it will forward it to the internal LAN address it is actually at. If your firewall admin has a clue what they are doing. they'll know how to do that. The hard part will likely be getting permission to do it.