The most efficient methods of applying stain are by wiping or spraying. Brushing is very slow, often too slow with water-based stains that dry rapidly.
When you have wetted a given surface with the stain, quickly wipe off the excess. With water-based stains, try dividing large projects into smaller sections to give yourself enough time to get the excess wiped off before it dries.
Wiping the stain on the wood is my usually preferred method because spraying then requires doing a thorough cleaning of the spray gun. Of course, spraying could be a good choice when staining large or multiple projects with the same stain.