OK...the first question is - do you want your sights to co-witness with the weapon at all times, or do you want them to be completely out of the way?
If you don't mind them co-witnessing with the optic, then there's really only 1 good way to go.
There's 2 kinds of co-witness. Absolute or center, where the iron sight system is centered in the view pane of the optic, and lower 1/3, where the irons align in the lower 1/3 of your view through the optic. Lower 1/3 obviously gives you a less obstructed view.
1/3 is the way to go. Next, you have to decide how quickly you want to be able to deploy your back up irons.
The fastest setup is to keep your standard AR front sight, and install a non-flipup rear sight. If your optic dies, there's nothing to deploy. The drawback is, there's a bit of clutter in your view. Some people don't mind, as the whole purpose and advantage to using a dot optic is not having to line up sights, not so much having a totally clear view.
The 2nd fastest setup would be to keep your front AR sight, and install a rear flipup sight. If your optic dies, the only thing you have to do is flip that sight up. That can be done pretty quick. This is the set up I use. You get a good view with less obstruction. I have lower 1/3 and when the rear is down, I don't see much of the front sight and it works out well. The ARMS rear springs up and you can deploy it while staying in your shooting stance....
The slowest would be having flip up sights in the rear and front. Takes 2 steps, and depending on the model of sights - might require that you get out of your shooting position. The advantage here is a totally unobstructed view. This is probably the most expensive route, as you have to buy the front flipup sight...
Where the irons co-witness is a function of the optics mount. The optics mount dictates how high or low the optic sits in relation to the irons. The irons are a constant (there are a few exceptions like short irons for use on rail systems).
IIRC (going by memory here) the EOtech mounted to the flatop directly will give you the center co-witness. You need a mount like the Larue to rise it up for lower 1/3. For the Aimpoint, the ARMS ones give you center, the Larue gives you lower 1/3. IF you decide on that route, be sure to ask and get definitive answer as to where the co-witness will stand. Don't settle for answers like "just right" or "perfect"...these mean nothing. There is a lot of confusion out there on the subject because many folks don't know the difference or do not know how to define them. Different brands of mounts have different heights.
I have the Larue/Aimpoint mount, and it's lower 1/3, use the standard AR front sight, and have a Troy flip up for the rear.
Goodluck.
