I'm not terribly familiar with how to manually run a profiler in eclipse. You might want to ask on the eclipse news group. Very sorry.
You would profile the JBoss Server in the following way:
1) download TPTP and find org.eclipse.tptp.platform.ac plugin for your OS
org.eclipse.tptp.platform.ac.win_ia32_4.4.1.v200806171132 - TPTP 4.5.0 Windows 32 bit
org.eclipse.tptp.platform.ac.linux_ia32_4.4.1.v200806171132 - TPTP 4.5.0 Linux 32 bit
2) add <PLUGIN_DIR>\agent_controller\bin to the PATH variable on windows or <PLUGIN_DIR>/agent_controller/lib to LD_LIBRARY_PATH on Linux
3) call SetConfig.bat on Windows or SetConfig.sh on Linux.
These scripts are placed in the bin directory.
If you have some issue with jaxp, it is probably caused by your JDK.
What JDK are you using? What error are you getting?
4) Start Eclipse
5) Open the Launch configuration of the JBoss server and add -XrunpiAgent:server=enabled to the VM arguments tab
6) Start JBoss Server
7) Open the Profiling and Logging perspective and call the Profile Configurations action
8) Create a new "Attach to agent" configuration, select some data collector in the Agents tab
9) call Profile
In the meantime, I solved JBIDE-2093. Hoping that the profile action will be available in some next JBoss Tools version.