You can install it either method you want. As long as the epo agent on the exchange server is talking to epo, it will get the policies configured in epo for msme. So if you upgrade the client, you need to upgrade also the extension in epo for it and make sure the policies are configured the way you want them to be. You don't link anything, it is the epo agent that gets policies from epo for any product installed. You just have to have the right extensions in epo for that product and assign the appropriate policies.
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