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Chase, this is the way I've been doing it, though I've recently switched from using the "wet water" to 70% Isopropyl alcohol (rubbing alcohol), as it seems to work much better. If you;re using tacky glue, make sure to water it down 50/50 or so. http://modelrailroadtips.com/index.php?op=Articles;article=32
A good idea is to paint the roadbed a shade of gray to match the stone color.(this saves on ballast by hiding missed spots)...Then spread it thin and use finger/ brush to spread it evenly...then mix some water, a drop of soap(dish detergent), and a little alcohol in a spray bottle. then wet the ballast....next mix Elmers glue with water and (can do in a glue bottle 50/50) and spead it down the center. The soap breaks the elasticity allowing the glue to spread and not clump it up. (If you want) you then can mix alittle plaster paris and black/brown powdered tempra and brush the center to give a darker color and hit it with water to seal it in...make sure to keep the inside of rail clean of ballast.