Getting a java server to work with Apache is painful, unless you you use one on port 80, and the other on port 8080 or something. If this is just for development purposes, that is the routew I would take. You cna not have them both listening on to the same port. Apache needs to get the requests and pass the pertinent requests to the server. My last server had Tomcat with Apache, and it took me weeks to get the connectors working properly, and then a while longer to get the rewrite rules so that the proper domains went to the proper server.
Ummm... Netbeans should have Glassfish with it already, assuming that you are using 6.1 or better.
and is there a best way to develop your development environment?