To avoid having ballast stuck to the sides of the rail or on the tie-tops, after you've applied the dry ballast (I use a paper cup to apply the ballast, squeezing and tapping it as I move it along the track), use a soft 1/2" brush to smooth it out between the ties and along the shoulders of the roadbed. When you've got it arranged to your satisfaction, flip the brush around, and lightly grasp it by the ferrule, laying the handle across the top of the rails. Using your free hand, rapidly tap the handle lightly as you move the brush along the track - the errant ballast on the tops of the ties will "magically" disappear, bouncing into the area between the ties. If you have an area where the track is on a fairly steep "fill", paint the slope with undiluted white glue before applying the ballast or cinder sub-ballast. When you spray with the wet water, the glue will be drawn up into the ballast. When applying ballast around turnouts, keep the level below the tops of the ties, especially in the area where the points move. Don't apply any ballast in the space where the tie-bar is - paint the roadbed grimy black here, as most prototype turnouts are quite greasy in this area. After the dry ballast has been levelled, and you've used the brush "trick" to clean the ties of ballast, but before applying the "wet" water, apply some LaBelle plastic compatible oil to the tie tops over which the points move, then flip them back and forth several times to spread the oil. Park the points in mid-throw before applying the glue mixture - this will further help in avoiding having them stuck in place.
I use "wet" water from a sprayer to wet the ballast, as I almost always apply the lineside scenery at the same time as the ballast. Depending on the site, this can extend some distance from the track. One of the most common mistakes when ballasting is to apply too little "wet" water - it has to penetrate right down to the roadbed or scenery base in order for the glue mixture to be drawn in completely. Too little results in the glue staying in the upper layer of ballast, forming a hard crust which isn't securely fastened in place. The first time that you need to vacuum your track area (trust me, the need will eventually arise) you'll be left with the need to re-ballast, too. Because some of my track is on fills of rip-rap and cinders, the amount of water and glue needed can result in drying times of up to a week - there's always pleny of other stuff to do while you wait. Here's a few pictures:
Ballast atop cinders atop coarse rock atop rip-rap - over 1/2" deep in spots:
Another area with the same layering treatment - the field to the left was a lake of glue for a few days
Ballast atop cork on the mainline in the foreground, with cinders, dirt and weeds directly atop the plywood sub-roadbed for the industrial sidings:
Mainline atop cork, with a small amount of rock and cinder fill beneather the ballast:
Ballasted track atop plywood, with cinders, then weeds spread along the edges, to give the illusion of a slightly built-up roadbed - all of the track and ground cover is at the same level, with only the "water" area actually being lower: