When it comes to writing, I was always under the impression the showrunner set the arc up, came up with an episode description, say about a page long, then handed out the assignments.
The showrunner can do it whatever way they want. Like the X-Files guy would write the important alien episodes, season starters and finales and the good episodes would just be one offs in between. I have a feeling that's how Doctor Who is done now with maybe just a hint of season long arc in it.
(I'm really bad at names.)