FYI I moved this question to the appropriate forum.
Not 100% clear on the issue, but you'd have to change your agent mappings so that the agents know which profile you want to map them into. The agents will be mapped when they startup and are placed in a system profile based on whether their name matches an existing agent mapping. Please clarify if that doesn't help.
You can also copy and paste agent groups from one profile to another. This might help you move agents to another profile. Just remember to delete the old agentGroup from the old profile, else the agents might map to the old profile next time they start.
@Ramakrishna D. are you trying to agent mappings from both system profiles to show up in a single transaction flow? If so, you might have to move the agent group to one profile as Joseph mentioned below. If that is not what you are trying to accomplish could you please explain you question in detail.