When working with stain, the easiest results are achieved by applying the same finish everywhere. Stain is much thinner than paint (in fact it's like water), and creating clearly defined cut lines and transitions of colours can be challenging, so once you get started, it's easier to just keep on rolling. The application instructions will tell you to roll it on, let it soak, and then wipe it back with a rag. I have always preferred to apply it, even it out with a brush, and not wipe it back at all. But experiment with a few scrap boards first before you start and make sure you've got the look you want before you get started.