Resolution: BW itself is just a Java application. It should work the same as other configures other Java applications to be profiled by JProfiler.
1). The JVM parameters needed by Jprofiler can be added to java.extended.properties in bwengine.tra .
2). JProfiler JAR files can be added to PATH and CLASSPATH in the bwengine.tra file. Make sure it is added in the following.
tibco.env.CUSTOM_EXT_PREPEND_CP
tibco.env.PATH
tibco.env.LD_LIBRARY_PATH, tibco.env.LIBPATH (if on UNIX environment)
3). Start the BW engine from the command line.