There are essentially two different types of things you can draw in Opacity: pixels and vectors.
Vectors allow you to draw content that will be drawn sharply at any resolution. Because of this, they are the recommended way to create images. Most of the Tools in Opacity create vectors.
Sometimes, however, you need to make tweaks to an image at specific resolutions. This is where pixels are useful. You can add or remove a few pixels here and there (using the Pencil and Eraser Tools) to make your image look perfect at all resolutions. You can always change vectors to pixels by rasterizing them. You cannot, however, convert pixels to vectors.
When there are pixels and vectors in the same layer, the pixels are drawn in front of the vectors.