In a large mixing bowl, combine flour, salt, ginger, nutmeg, and sugar. Add rapid rise yeast and whisk until incorporated. Make a well in the dough, then add water. Use a wooden spatula to combine the dough into a batter, but do not overwork the dough. The batter should be wet and sticky. Cover with a clean kitchen towel and allow batter to rest on the counter until dough doubles in size, about 1 hour.
Prepare the ginger thyme sugar. While the batter rests, combine the ingredients for the sugar on a large plate. Toss to combine. Set aside.
Heat oil in a large frying pan over medium-low heat. The oil should rise to about 1-1/2 inches.NOTE: It is important to use medium-low heat to ensure the oil heats evenly and to prevent the puff puff from burning. Test the oil by dropping a small amount of batter into the oil. The oil is ready if it starts to sizzle and the batter rises to the top. Once the batter has doubled in size, use an ice cream scoop sprayed with cooking oil to spoon batter into the hot oil. Use about 2tbsp of batter per puff puff. Working in batches of about 4-5 puff puff at a time, fry puff puff for about 2 minutes per side, making sure not to overcrowd the pot. Use a slotted spoon to transfer cooked puff puff to a plate lined with paper towels to remove any excess oil.
Transfer puff puff to sugar while they are still warm and toss to coat. Serve warm.