Do you mean "consolidate" or do you mean "separate"?
I'll assume you mean the latter.
There is no direct way in ConfigMgr to move updates from one package to another. It's easy enough to do though, just create new packages, download the updates you wish to move to the new packages, and delete the updates from the old package. If you wait until after the new packages have replicated to the DPs before updating the old package, the content won't actually even be copied to the DPs because of the single instance store.