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It doesn't really matter, provided you have clearance for your scope to get down as low as you wish. Many imagers do not bother imaging below 40 degrees altitude due to atmospheric effects. Everything rises in the East and in the Southern hemisphere the sky rotates around the south celestial pole. My personal preference is north south Long axis alignment for my observatory, with my mount more towards the Southern end of the observatory, giving me room for my workstation area in the northern end. Roof rolls off to the north, and can be stopped over my workstation, an important factor on damp nights. Importantly your wall height and pier height must provide you with the ability to reach down to the altitude you desire, and you must have swing, slew, room for all your gear within the narrow dimension.
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