I did some for a "circus" themed party. I used the NFSC recipe and divided dough and colored it different colors. You take parts of each color and roll into a "snake". then you combine with some other colors and make a "lollipop" by swirling them. I put the stick in prior to baking and just let them cool off completely before picking them up. They looked awesome and didn't need the extra sweetness of the icing. Just make sure you flavor your dough. HTH!
To get rid of small bubbles, I use a straight pin. It prevents leaving craters in your cookieAnd in regards to the order of decorating....I usually flood a solid color and add detail. Sometimes when you have a cookie with lots of detail layering the colors can sometimes look awkward due to the outlines. I really think personal preference and what your decorating will be the deciding factor....good luck