I have the tcp ports discovered, I have the webservers discovered and also the host that hosts the webservers are discovered. I want to know how to show that the application servers and the webservers communicate via 8443.
If the sockets are not "long lived", you will be unlikely to be able to catch the client side of the socket "ESTABLISHED" from a netstat/lsof point of view. If that's so, the P2P patterns will be of little use to you.
If that is the case, you need to write a pattern to interrogate the client side (in this case, the app server) for its connection parameters. .ini, .xml, db contents, registry, that sort of thing. If you go through a load balancer this can become even more twisted. As far as API dependencies, again you're _probably_ on your own. Have done this before with Java .jar files with strict naming standards, stuff like that.
Get on to HP and ask for the DDM developer guide, and possibly "Discovery 101". These (when I saw them last) were incomplete but very, very useful things to have around.