It's hard to explain how to use them, but it's not hard to do. I run my Eotech co-witnessed (same plane), but when I'm shooting, all I see is the red dot on the target. I don't have my cheek all the way down like when I use my irons, so the irons are both "under" my line of sight AND out of focus. If I need to take a longer shot, or a more precise one, I get down on the stock and can still use the fine 1moa dot of the Eotech through the sights and slow down the shot.
For those who mount their red dots slightly higher than their irons, they can't get a good cheek weld and still use their red dot. They will then need to use their irons (hopefully it's not a low-light situation.) I understand their desire to use there red dots without the irons getting in the way, but I think if they set up their sights like mine (same plane) and USED them, they would see it works quite well.
Of course, the Eotech is accurate anywhere in the display box, not JUST in the center.
Here's one of my setups: