Yeah, i would unpack one pack and update with it, then unpack the next and update with that til you get them all done.
Reason being the way that the updates work. For example you could have
Update 1 with gamerom.zip which contains files a,b and c
Then in update pack 2 you could have an update to gamerom.zip but only contains file b.
Now if you unpack them in the updates in the same location gamerom.zip from update pack 2 would over write the one from update 1 but it only has file b and not a and c.
Hope that makes sense.