Start by using a paint brush to 'cut in' or stain the edges and the corners. Use nice, long brush strokes, and blend in as you go. As long as you are continuous, it won't matter if the stain is a little stronger in some parts. Once you've finished cutting in, remove the masking tape before the stain dries.
Pro tip: If you want to go the extra mile and stain in between the boards, now's the time. Just use a kitchen sponge or scouring pad, fold it if necessary, dip it into the stain and run it along between the boards. Make sure you wear protective gloves for this part!