Hi welcome to Health care magic forum.
Thanks for choosing H.C.M.F.
Your 11 month old son is screaming in pain, feeling pain when you touch his nappy area near ball sack, and also while pooing.
It appears to be the nappy rash
that is causing pain, caused by loose motions , as the motion contains seeds it represents indigestion
, and stomach pain also would have been there.
The stools is smelly and runny, so it must be with lot of infection.
I advise you to consult a pediatritian for diagnosis and treatment. You may have to get the stools examination for bacteria, and reducing substances, besides other routine tests for confermation of the cause.
If reducing substances are present lactose containing foods should be excluded from the diet of the baby.
Wishing for a quick recovery.