I've done a lot of spot staining in cabinetry, furniture, doors, etc...but none specifically on kayaks as you mention. When spot staining I would simply use appropriately darkened, or darkening, stains, dab it on with a brush, Q-tip, or toothpick...whatever it takes. Let it stand for different times and wipe off. It's eaisier to try to darken slowly...in little leaps...rather than one big jump. This works with penetrating type stains. Laquer stains, and the more opaque type, are a bit different in that they penetrate a bit, but also cover a bit. With that type you try to mix the color and then apply, and wipe off...or not...as the case may be. As much as everyone wants a perfectly done kayak, it doesn't happen. I wouldn't worry about the stuff others can't see.