This is the way I approach them: My 2 cents
When using iron sights I focus on rear and front individually to line them up. A good cheek rest should minimize movement between the rear and front sight once set. Then I focus between the front sight and the target. Last focus on the front sight. It's a very dynamic process of checking and rechecking alignment of all three.
Red dot focus on your target and bring the dot to it and have both eyes open.
Haven't used an ACOG, but if like other scopes they have everything in the same focal plane so both are in focus.