Modify Style Manager programmatically

My Java application runs on SunOS 5.8. Our use of a 3rd party class
requires us to modify the Style Manager-Window setting "Allow Primary Windows On Top" - the default for this is on, we need to turn it off.
Is there any way for our application, or our installation, to modify this setting? We would prefer to not rely on a release note that may or may not get read and followed.

Thanks for any hints,