I had trouble keeping both eyes open on the EoTech myself. I had the best results by simply "retraining" myself at night. I mounted a Streamlight TLR1 on the rail, and kept both eyes open while getting accustomed to the halogram.This worked reasonably well, but not 100% - as I couldn't do any live fire at night to assure my concept was working.
Eventually, it took a couple range sessions to get used to teh EoTech, but what really hit the proverbial nail on the head was using iron sights to co-witness. Once I did that, and then dropped the rear sight - the rest was easy.
I bought an Aimpoint Comp (ML2) and figured it would be easy, but NO - I feel like that thing is a scope and my sub-concious kicks in.
Bottom line for me? Hell, at the risk of drawing criticism for this statement... just shoot the way you are the most accurate and have fun. If we ever have a true SHTF scenario, it won't matter one way or another if you use one or two eyes.