In my experience, longer distances come through conditioning. You ride longer, spending more hours in the saddle, until your body gradually acclimates to it. I still start to get some discomfort in the saddle out past the 4 hour mark now and again-- but at the same time, anything short of 2 hours on the bike barely feels like riding at all. Unless the saddle is giving you actual pain, it likely just needs a little tweak in the fit. A little discomfort from a ride double your typical length is to be expected.
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