Wait until you expect to have two dry days in a row, then apply a stain or sealant. Be sure that your product specifies that it repels water and resists fading, or you'll find yourself repeating the process in short order. Cover nearby plants and structures with plastic so they won't get any of the stain on them, then apply the stain to the deck using a paint roller.
Use one thin coat at first, being sure to even out any puddles that form as you go, then apply a second coat, using a paint brush to get to areas where the roller won't reach. Be sure to let stain-soaked rags dry in the open air before disposing of them, as evaporating finish is a fire hazard.