If you want to debug the execution of any initialization code in your server you can do this. Initialization code is set up with the KernelInitializationCode configuration parameter in the MSPConfiguration.xml file. When you launch the server in debug mode, if you set the DebugWaitLimit configuration parameter this will cause it to wait for the specified period. In the following example the server will wait for 100 seconds.
<MSPConfiguration> <KernelPool> ... <DebugWaitLimit>100000</DebugWaitLimit> </KernelPool> </MSPConfiguration>
This gives you time for the debugger to connect, and then any breakpoints that are set in initialization code can be activated. For this to work, you need to have a copy of the initialization code in your webMathematica project.