being as it's summer months, i know several people who, to temporarily solve heater issues, will loop the system, making it so no coolant goes through the heater core. but, to allow us to help you better, what issues are you having, exactly?
sounds like its time to buy a different brand of heater core
as for hose connections, if one is above the other its best to have the hose from the top port to the water pump, and the one from the bottom port to the head. otherwise there's a chance of an air pocket getting stuck in there - but i don't remember, maybe they're side by side, in which case it doesn't matter at all.
There's been quite a bit of discussion on here about heater cores, but most of it has been regarding them fitting rather than leaking. If you are getting new ones that leak I would find a new source. But, there aren't very many different sources in reality.
The heater cores are very thin and can't take much abuse from taking the hoses on and off. If you ever need to replace the hoses on a old but good heater core, always take a knife and cut them off the heater core barbs, never twist them off. It will leak every time if you twist them off, been there done that.
Factory is the easiest. I got mine from Archion, also known in real life as Matt Vose. PM him and he can fix you up. But this thread has info specific to your truck, as mine is an 81 Ranger with factory air as well.