Entirely depends on what specific effect you are looking fro. From simply lowering the opacity to using complex blending mode techniques this could be anything. Impossible to be more specific without knowing what you actually have and what you wnat it to look like.
AE has a transparent background by default so if you make an animation of a flag it will already have transparency.
Stupidly, and to confuse new users, they choose to hide the hide this transparency with a fake black background that does not render. It's part of Adobe's "anti-logic". At the bottom of your comp window there should be a little a button that looks like a checkerboard. Click it so it turns light blue. Then you will see the transparency that they stupidly choose to hide by default.