I am using an Intel Core i3 540 and I have disabled the AMD Graphics Device.
Now, how can I activate the Intel HD Graphics so I can use Intel GPA?
After a reboot, bring up the Device Manager and open "Display Adapters". You should then see the HD graphics appearing in the list, which means that it's available. Then download and install the latest HD graphics driver (instructions are here), then startup Intel GPA Monitor and run gpasample.exe or your own graphics application.
Also, Intel GPA can analyze games using AMD graphics as well. However, using Intel GPA with Intel Processor Graphics you'll be able to see more metrics. The Intel GPA help file shows the difference in what metrics are available -- see the "Metrics Descriptions", then look for the section "Metrics List...". So the choice is yours as to which device is most useful for your analysis tasks.
Hopefully this has helped. In any case, please let me know whether Intel GPA runs on your system -- if not, please post more info so that I can get you up and running.