Get your baking soda (and whatever type of soap, I use dishsoap)
Put everything in a bowl with your shoes and some water. Swish everything around every so often. Change the water every so often, adding more soap and baking soda each time.
You're done when the water stays clear. Just gotta mention, I do this for cheap flats only, don't ruin your fancy shoes. If you do it's on you.