Running it inline should be fine unless there is too much restriction. I mean, what difference would it make if the filter plugged up? It would be a whole lot easier to change the filter than fiddle with the heater core. However, the bypass arrangement should work too, it isn't like the coolant is going to be picking up "chunks" at any great rate, and if the theory that "all the oil gets filtered eventually" as many people believe is correct about a bypass oil filter. I can't really see why the theory wouldn't hold true in this situation. But you can't use them to "clean-up" a coolant system that is thoroughly plugged, you still need to start with a clean block, and you would still probably get a whole lot of junk for a while.
