Your post is a bit hard to parse, so I'm just going to tell you how I have mine set up:
Two RFTools Shield Projectors. Red Shield templates for the floor, then the walls and ceiling as blue. 5x5x5 interior. Projector for floor is solid for everything, Projector for walls and ceiling is set to pass for players, and SolidDamage for hostile mobs.
^This can be replaced by your wither containing and killing system of choice.
Inside the wither containment system, I have reinforced obsidian in the wither pattern (1 block, then 3 blocks above, then 3 blocks above), one block back of center. You'll want to note which cardinal direction the center is relative to these blocks.
Outside containment, I have seven phantom placers, bound to each of the reinforced obsidian and set to pulse. You can either load them up directly with the relevant item or pipe it in however you wish.
Now, to control it, I used EnderIO insulated redstone conduits, one channel for the soulsand placers, and another for the wither skull placers. The reason I have two separate channels is that I had issues with the placers if I didn't slightly delay the placement of the skulls after placing the sand. In my case, I had a Super Circuit Maker circuit with a Quartz Resonator to delay the redstone signal to the placers for the skulls. Very simple circuit, just an input, a straight connection to an output, and a split off to the side for another output with a resonator in between, set to a delay of 5 ticks.
Hope that helps a bit.