Apply your color using a randomized approach. A systemized approach will look too "packaged." Apply one color at a time.
When you start an area, finish it. Stagger areas rather than working in a straight line to prevent definition lines.
Highlight colors are best hand-applied, not sprayed.
When working with reactive stains, be careful. If you start at the top and it runs, the runs will be permanent.
When applying chemical stains, hand-held spray bottles can be used for detail work. Sponges can be used to agitate the stains into the nooks and crannies of the texture. Artist paintbrushes can be used for intricate patterns.
Don't want the grout joints stained? Pre-seal them with a clear acrylic sealer. It resists the stains.
If coloring a brick pattern, use a roller to apply the color instead of spraying to keep the grout lines uncolored.