It can be done so many different ways, no one is the absolute right one. In fact, I have a very clean cab on a truck I have that I use very little and it has an AC setup in, a rust free 79 CAB. And I wanted to put AC in my 79 Bronco and was looking at my options, one of which was swapping a lot of parts between the two trucks and just updating the heater cores on both as I replace, replacing and updating the R12 components in the parts to go into the Bronco with 134A compatible parts (easy to do, though I like working with 12 better - just my preference), and making the necessary extra cutout in the Bronco and tinning up the extra holes in the truck cab where I leave the holes where parts once were, to even just building up my own plenum with a selector for the heat control and defrost/AC functions. It's not as hard as you'd think if you make the transitions smooth and diffusers work correctly, as well as source out controls for everything and adapt a controls assy. Being a seasoned tinner and AC guy it's possible providing a lot of precautions and insulating is done. However...
As pointed out, there are many really good aftermarket companies out there that will give great performance without the ghetto look. And even one company, can't think of the name off hand, where the components take up less room under the hood than stock which means more room for turbo's, engine swaps, and many other goofy ideas we come up with late at night as we sit trying to sleep.
Which one to choose? Of course that's up to you, your talents, and of course your wallet. But I would go for the best performance since diesels kick out butt loads of heat and those of us with diesel conversions as well as stock diesel trucks aren't always insulated in the cabs as well as we should be.