I wouldn't. I'm not sure how easy it would be in any event, since server.xml is an XML file digested by Tomcat, not a general-purpose script.
However, if you create a file in the TOMCAT bin directory named "setenv.sh" (Unix/Linux) or "setenv.bat" (Windows), you can assign environment variables in that file and the catalina script will use them.
The file format is the same as any other script file that sets environment variable values.
An IDE is no substitute for an Intelligent Developer.