Finally someone finds this a problem... Indeed SU website will not price stopovers using a through classic/ flex fare (with some rare exceptions). You need to call to book it. Pathetic for a country that needs stopover tourists.
Or you may also manually modify the flight dates/ numbers in a search line and paste it to a new window - this will do the trick (this will be the screen after you select your last flight). You should using 2 segments in this case (=RT), for example, NYC-HEL and HEL-NYC. Adding segment 3 will ruin everything (SU will offer ridiculous fares in classes B, W, D and above which are not even flex as there is always a cheaper classic option for all booking classes...).
Feel free to PM me if you still need help.