Seriously, I've found that if you see two targets, and just can't fix it, you will probably have to try closing the non-master eye until the problem clears up. Some people just can't shoot with both eyes open. Remember, you need to check yourself and make sure that you aren't trying to shift from the front sight to the target and back again. With your focus properly on the front sight through the shot, the target will naturally blur just a bit.
I had the same problem. Being cross-eye dominant (right hand, left eye) I think for me it would be the left one, not sure.
Perhaps you could start at a close range (about 3-4 yards) so you have less "two target syndrome" and see where you're hitting. I think if you start at a closer range and start moving out as your accuracy improves, your brain will program itself to aim at the right point. I believe that's what did it for me. One day it just clicked, front site in focus, see muzzle flash, shots on target. There are plenty of people here who could tell you better, just letting you know what I think did it for me.
My eyes switch once it gets to dim light (strong side dominant in light, weak side in dark). Finally resorted to partially closing weak side eye all the time. That blurs out the target, but you still have some peripheral vision to pick up movement. Might give that a shot.
Another thing you could try would be put a piece of semi clear tape, like 3m scotch tape, on the lens of your non dominat eye shooting glasses, or your regular glasses if that's what you wear while your shooting. I've seen alot of bullseye shooters do that, and supposedly it works really well. May not be for you, but might be worth a try... good luck.
When shooting quickly at close to mid-range targets I shoot with both eyes open and focus on the spot on the target where I want the bullet to land.
I am right handed and right eye dominant, but if I think about it there are two sets of sights when I do this. It really doesn't matter, if you get either set of sights lined up on the target you will get the hit. For me, the extra set of sights to the right are the left eye set of sights.
After enough practice you will easily be able to ignore the "wrong" set. Your only risk with this method is trying to line up the rear sight on one set with the front sight of the other set. Of course if your arms are of normal length the gun will be nearly sideways. Unless your eyes are too close together.
The only time I focus on sights is for lining up very long shots; whether for pistol or rifle. I apply the same principle for practical rifle and pistol.
I drive a car the same way. I suppose some people focus on the hood ornament or left front fender and get around that way. I focus down the road on the point I want the car to pass through. I use peripheral vision to line myself up with that target.
Focus on a spot on the target, bring the gun up through your peripheral vision into your line of sight until one of the sight sets is on the spot then squeeze.
It was odd at first, but when I'm "on" I don't actually remember lining up sights on the targets, I only remember focusing on the impact points and seeing the holes appear. Give it a try.
I shoot with both eyes open, but because I have cross dominant,(righ handed, left eye) I find I need to turn my head at 45 degree angle to line up my left eye with the front sight with an isosceles stance.