Read up in the manual on using render layers. Or if you want a visual guide, you can take a look at Rage's Introduction to Compositing tutorial here.

If you're comping several scenes instead of layers, just make sure you have something that represents the same scale (like say a cylinder representing a human) in each one so proportions are correct in the end. It's easier to just use layers and turn off what you don't need to see while modeling, then render things out in layers.

Compositing app is just a matter of personal preference whether it's AE, Digital Fusion, Shake, or Combustion.