The male flowers will be on a longer stem then the females, the females will have the small fruit below the flower. To hand pollinate pick the flowers from the plant and remove all the petals, then open the female and rub the male around inside the female.
I do this even with my outside garden. The trick is to know the males and females are ready. The flowers will start to change color the day before they open, when they open the best time to pollinate is in the morning.
I grow giant pumpkins and you always hand pollinate them.
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