Yeah, seat height and fore/aft position (and handlebar position) are more important than design.
Seat height is especially important for knee pain -- having the seat too low is quite hard on the knees (as is pedaling in too difficult a gear).
For the back, seat position fore/aft and handlebar position (both up/down and fore/aft) determine how much the back is stressed. Generally a more upright position (seat and handlebar closer together and handlebar higher) is easier on the back, but seat and handlebar too close together can "scrunch up" a tall person and cause problems. (And if you have an excess of avoirdupois having the handlebar too low can make it hard to breathe well.)
The main thing that seat design can do for you is relieve (or not) pressure on sensitive areas, indirectly relieving the back since you don't contort yourself so much to take pressure off the sensitive areas. But it often turns out that super-padded seats and (especially) seats that are extra wide are less comfortable than their more Spartan cousins.