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I suppose you have already gone through following document
In case you have any specific questions/issues please let us know.
Biztalk has components built in both C++ and .net. .Net agent would not be able to instrument unmanaged code in Biztalk(c++). Which restricts .net agents ability to add visibility on non .net components.
When some application makes the exit calls to biztalk is important point to track and that is why .net agent supports WCF Send Port or the SOAP Send Port.
On recive ports the messages are recieved and processing is done inside an unmanged part of the Biztalk, which mostly can not be tracked by .net agent.
Using the BizTalk performance counters you get some more insights into overall Biztalk execution.