Your PHP and JAVA will live entirely separate lives. If you want you can even use Tomcats mini web server to serve up the JAVA pages without going through Apache. This would mean using the 8080 port but it'd keep everything separate.
If you don't want to do that, and most people don't, then look up mod_jk2 it's and Apache module that will allow Apache and Tomcat to talk to each other. It was very easy for me to set up and hasn't once affected my PHP pages that are running on the same server.
The basic steps are:
1. define a worker, just some settings that tell apache where tomcat is.
2. link a directory to a worker, this just tells apache that you want anything that comes into the specified directory to be sent to tomcat for processing.
3. reboot apache. Apache is now done and ready to talk to tomcat.
4. Setup tomcat following all of it's directions.