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I would think that lumping the updates together would be fine, but it would be nice to see some feedback from others using Shavlik Patch to see if there are differences in preferences out there.
Also, can we target all systems with our 3rd party application deployments like we do with Microsoft updates and only the applicable updates will install on a corresponding systems?
Yes, the updates should only apply when needed. There isn't any software distribution logic in Shavlik Patch so there wouldn't be any worry of an application getting installed that is not on the system - just updates applied to applications already installed on the client systems when needed.
Hopefully some others will chime in with some feedback concerning your first question.