"Now I put the sugar in the cup" means that what you're doing at that moment is part of a general procedure. For example, if you're showing someone how to make a cake and you're putting sugar into a cup, saying "Now I put sugar in the cup" means "Every time I get to this stage (of the cooking process), I put sugar into the cup". "Now I'm putting sugar into the cup" is simply a description of what you're doing at that moment.