The Internet architecture has recently shifted towards a framework characterized by multiple interconnected cloud sites, all linked via an L3 IP network. With this shift, managing networking controls among multiple cloud sites is becoming a significant operational challenge. In particular, ensuring effective networking control necessitates a deeper understanding of flow-level dynamics for comprehensively monitoring interconnection statuses across multiple sites. In this paper, we first propose an IO Visor-enabled tracing solution for Linux-based boxes to efficiently enable the comprehensive collection of network packet flows across interconnected sites. Next, we apply IP prefix-based flow-level analysis at a centralized location to support the intent-based networking control application. This flow-level analysis involves generating policy-based specific action (i.e., redirect) via SDN controllers for specific source IP prefixes, which are causing unknown or potentially vulnerable flows. Furthermore, we employ an open-source ONOS SDN controller to tackle the challenge of managing the hybrid SDN-IP interconnections. By leveraging intent-based networking control, we effectively apply ONOS intents based on IP routing information and generated a set of forwarding action. We evaluate our proposed solution in an experimental SDN-cloud testbed, demonstrating its effectiveness in real-world scenarios. Overall, through the seamless integration of these monitoring and control approaches, we manage to enhance the adaptability and security of the interconnected cloud sites of the testbed.