Once Trusted authentication is enabled from CMC and TrustedPrincipal.conf file downloaded under <INSTALLDIR>\SAP BusinessObjects Enterprise XI 4.0\win32_x86, nothing has to be done on the BO side.
Now, if your COTS application is on the same machine as BO, you do not require any additional configuration for your java application as well. If your java machine is on a different machine, you would need to copy the TrustedPrincipal.conf file to the machine where your java application is and follow the instructions given in my earlier post.
No SDK plugins are required to download, you have the SDKs installed with the installation of BO server. Share the required jar files with your application team so that they can use the jars in your COTS application.
BO jars can be found at
<INSTALLDIR>\SAP BusinessObjects\SAP BusinessObjects Enterprise XI 4.0\java\lib
Thanks,
Prithvi