I do it up the gears most the time. And every now and then down as well (I have a slipper clutch so it makes it much easier to go back down)
A quick shifter just uses electronics to do what you are doing manually but it does it much much faster. If it was bad for the clutch they wouldn't use them in racing or be now factory fitting quick shifts to new bikes. Some quick shifters also support up and down so it should be no issues with you doing it manually either.
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