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I started out going for top aligned today but was rushing to rip the ply i was fixing to the studs to help reinforce things and used the narrower of the screens for reference for its width so when it came to mount the tv it was too narrow to mount the second one low enough without the bottom screws going off the edge. so went for middle and i'm happy with how it turned out.
need to get the cabling all sorted so i'll be taking them off and on a few times still before i tighten the mounts up fully so they're a little misaligned for now but they sit dead level when properly seated.
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Honestly I think it's down to personal preference. I use 2 monitors that are the exact same, but 1 landscape, and 1 portrait. I have tried bottom alignment, top alignment, and center alignment, and I marginally prefer center. I think I'd be fine with any of them if I had to, though.
Best practice, of course is to make sure that your main screen is centred at eye level so you're not straining your neck needing to look up or down for long times.