I would clone the policy, create a filter, and then assign it to the target. Roll out the agent to a test group to ensure it behaves properly (using that filter and a clone of the policy), and then replicate this with a pilot group, and then move to production. Depending on bandwidth, hours of operation, an overnight roll-out could work.
How large is your organization? How many sites? What kind of links? There are obviously several inputs to this question.