Complex sentence: The main rebellions were of the Rajputs in Rajasthan, Malwa, Gujarat, Bundelkhand--only the three weak states of Amber, Bundi, and Datia were in Mughal service, and were being used mostly against their own Hindu brethren by the cunning Aurangzeb.
Split into simpler sentences: The main rebellions were of the Rajputs in Rajasthan, Malwa, Gujarat, Bundelkhand. Only the three weak states of Amer, Bundi, and Datia were in Mughal service, and were being used mostly against their own Hindu brethren by the cunning Aurangzeb.