Excessive padding can potentially make a saddle uncomfortable for longer rides. With a more upright position, a slightly wider saddle than you use on your other bikes may help, and slightly more padding might also help. If you need additional cushion, some options to consider would be wider tires, a sprung saddle, or a suspension seatpost. In my case, I'm stuck riding full suspension and upright, and actually get by with the same saddles I used back when I could ride a road bike. You might even try swapping the saddle from one of your other bikes to see how it works for you on the ebike.