With an optic like that Aimpoint, the dot is parallax free (well, for the most part). That basically means Mr. Bullet goes to the dot regardless of where the dot is inside the scope. That is why most people who use iron sights with something like an Aimpoint tend to look over the irons at the dot but then drop their head slightly to use the irons if needed. This keeps the sights mostly out of your way.
Ever heard "co-witness?" You can setup Aimpoint and simliar sights to be in-line with the iron sights so that the irons sit exactly in the center of the optic. Looking through the irons you'll see the Aimpoint's dot sitting on top of the front sight post. Raise your head over the irons just a bit and the dot is still visible (and on target!) but the irons are not in your way.
Some folks feel they loose too much field of view with this kind of setup and choose to mount the Aimpoint a bit higher so that the iron sights are in the bottom third of the optic's tube. Either way, when you look at the irons the dot will appear to sit on top of the front sight.
If you ever want to come play with different setups like this come join us at Creekside