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It's a good idea to get comfortable with using both. By default I'd go for the right eye, but it's good to swap. Sometimes your eye gets tired. Also the brain responds subtly differently and most people over 40 (and many much younger than that) have different degrees and types of eyesight defects in their two eyes. My eyesight is pretty good for my age but my left eye is slightly better.
Also with a right-angle finder it's very handy to be able to quickly jump between finder with right eye to eyepiece with left eye. If you're into star-hopping with a Dob, I'd highly recommend it.
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