Step 3: Apply stain - Get a drop cloth and place the tray above it to fill the stain. Ensure that your purchased stain products are perfectly matched with the color of your deck. Stir and mix it up thoroughly using a paint stirrer to make sure no bubbles are formed. Pick the right staining tool; the best to use are deck brushes. Apply thin coats on the top surfaces of your deck. Then, put in whether clear sealers or semitransparent stains. Repeat the application of stain until it gives a perfect look.