I use the JAVA_OPTS environment variable in catalina.bat - for example, here is part of the line in my catalina.bat
set JAVA_OPTS=-Djavax.net.ssl.trustStore="c
ata\Scrutiny\keystore\clientkeys"
Here is the comment from catalina.bat documenting the use
rem JAVA_OPTS (Optional)
Java runtime options used when the "start",
rem "stop", or "run" command is executed.
Bill