Another option is to provide the correct JAVA_HOME pointing to your version of Java. On ubuntu when using the packaged OpenJDK 6, you can add:
export JAVA_HOME=/usr/lib/jvm/java-6-openjdk
to the top of the 'funambol' startup script.
This way you can use the normal 64bit Java Runtime
More information about formatting options
Other option
Another option is to provide the correct JAVA_HOME pointing to your version of Java.
On ubuntu when using the packaged OpenJDK 6, you can add:
export JAVA_HOME=/usr/lib/jvm/java-6-openjdk
to the top of the 'funambol' startup script.
This way you can use the normal 64bit Java Runtime