If you use a water-based stain rather than alcohol, you get more time to play as water won't boil off at room temperature as fast as alcohol will. That allows you to rub around and fade things into each other more gradually. You can use water-based stains under solvent-based finishes as long as you give it plenty of time to dry thoroughly. You don't want any water trapped under the finish, unless your inventory of cuss words is low.
Also, if you're going to use water-based stain, wet down the surface before you start staining. That'll keep you from getting boundary marks where more or less stain gets absorbed.