With soft padded saddles you sink down, distributing the weight over your soft tissue and compressing blood vessels and nerves.
A proper road saddle is much harder and supports you at your sit bones , not the squishy bits between. You need to select a saddle which fits your shape since everyone is different. You also need to ensure that your riding position is suitable for more extended ride with a lower bar position to distribute weight from saddle to bars.
Putting the padding on the shorts prevents chaffing and sweat rash.