It seems that your red-dot scope is not parallax free, but you would have to shoot it and see. If the POI is always at where the red-dot is, no matter how your eye is lined up with the scope, then it is parallax free (this is a good thing).
Regarding how you would use the red-dot, it is really up to you. You can "cowitness" the iron with the scope or use the iron as backup. Check out this article
http://www.rifleshootermag.com/gunsmithing/ar_092105 .