I love to use my actual paint bottle as the tool for applying the "spots" of paint. First shake your bottle of paint with the lid close a few times to loosen up the paint. On the last shake hold it upside down for a second or two. Second, open your bottle of paint right side up, see the paint gathered on the tip of the top that goes into the base of the cap? This spot of paint is the perfect size to add little accents of paint to projects.
After I've adhered my layout together I add paint where it is appeasing to the eye by dabbing the screwed off top to different areas of the layout. Remember start with a little first, and then add more as desired by putting the cap back on and repeating steps 1-3.
(Supplies used on Layout: Studio Calico Elementary and Making Memories Paint)