I might be a bit late for the party but I follow below steps to make it fully configurable using IntelliJ's way of in-IDE app test. I believe the best way to go with is to Combine below with @BelusC's answer.
1. run the application using IDE's tomcat run config.
2. ps -ef | grep -i tomcat //this will give you a good idea about what the ide doing actually.
3. Copy the -Dcatalina.base parameter value from the command. this is your application specific catalina base. In this folder you can play with catalina.properties, application root path etc.. basically everything you have been doing is doable here too.