Japanese Maple seed is ripe when the tip of the samara is slightly dry, usually indicated by a brown necrotic look. They typically reach this stage sometime in October. Seed can be immediately sown in prepared beds or stored and then stratified for sowing in spring. I usually place mine in large, flat box tops, evenly distributing into one layer. I do this to dry the seed out. This occurs in my garage. When dry I place the seed in bags and keep in the cool, unheated garage until the stratification process begins. Stratification is a pre-germination treatment to break dormancy in seed and to promote rapid, uniform germination. The seeds are exposed to moisture at a temperature just above the freezing point (1-5 deg. C) for a specified time. Some seed require a warm stratification period followed by a cold period. Most simply require a cold stratification. Generally Acer palmatum seed require about 90 days, cold. I usually wait until Dec. 20th or so to begin stratification of my seed so that spring is just around the corner when my seed are ready to plant out.
When the time comes to stratify, I place the seed in large plastic cups, about 1/3 full. I then fill the cup with hot water, 110 degrees Fahrenheit, no more than 120 degrees. My hot water heater is set at about that temp so I simply run tap water until hot and go from there. After filling the cups with hot water I set them aside and let them cool for 48 hrs. When cool I pour the water off, through a screen so as not to lose the seed. I then take plastic baggies, the ones that seal real well, and I place the seed in the bag, about 1/3 full. I then add an equal amount of a roughly half and half mix of sphagnum peat moss and vermiculite to the bag of seed. Seal the bag and shake it up thoroughly. Once it is thoroughly mixed I add about 1/4 teaspoon of a fungicide, Captan (wear gloves and a dust mask, Captan, bad stuff). Other fungicides may work as well. I then mix it up again, thoroughly blending the contents. I next add just enough water to the bag of seed and mix to moisten, taking care not to make it wet. Just moist. No standing water in the bottom of the baggie. I then seal the bag and place it in the coolest drawer in the fridge. Ideally at about 38 - 41 degrees Fahrenheit. It sits there for about 90 days and I check it on occasion, making sure that it hasn't dried out. Within that 90 day period some of the seed should have pushed out a root radicle (the tip of a newly formed root). When a good proportion of seed have produced "radicles", I place the seed in a large bowl and individually plant each one in a 4" cup, 18 per flat. They are planted in, primarily pine bark fines, shallowly, just covering the nutlet. An ideal flat would have 18 little samaras, held upright, like little flags. Any seed not yet showing germination go back into the bag and back under refrigeration. I sometimes keep a bag refrigerated for two years. After that I sow the seed in a bed. Seed may germinate, sporadically for three years. Acer japonicum seed seems to germinate better in the second year of stratification. You could also, at this point, sow them in bulk in a prepared planting bed but I prefer planting them into flats. I have a friend in TN who produces thousands of seedlings and he basically takes large quantities of moist seed and places them in large black garbage bags in a cooler. There is no "one and only" way but this method works well for me.