Indeed, the shape and design of the saddle is quite important for longer distances. Proper bike shorts fit like a second skin and help to reduce chafing or rubbing, but the right choice of saddle helps to reduce pressure on soft tissues. Your weight should be supported on your sit-bones and not on anything soft inbetween. Typically a firmer saddle works out better in this regard than a soft padded saddle, although that goes against obvious expectation.