Tomcat comes setup to use 2 environment variables: CATALINA_HOME and CATALINA_BASE. One refers to the directory that contains all the parts of Tomcat that can be shared between multiple instances of Tomcat. The other is a separate directory for each Tomcat instance.
In the basic setup, CATALINA_HOME and CATALINA_BASE point the the same directory and both sets of subdirectories share that common root. In your case, however, you'd have a separate CATALINA_BASE for each Tomcat you're running and it would contain things like that Tomcat's conf/server.xml file, the webapps directory, work directory, log directory, and so forth.
The easiest way to setup JAVA_OPTS is to create a file named "$CATALINA_BASE/bin/setenv.sh" and define JAVA_OPTS in that file. setenv.sh will be executed ("sourced") as part of the startup and control functions provided by $CATALINA_BASE/bin/catalina.sh, which is in turn invoked by the Tomcat startup and shutdown scripts.
An IDE is no substitute for an Intelligent Developer.