Zooming right into your image is the only way to make subtle changes at the pixel level. Use Ctrl + to zoom in and Ctrl - to zoom out. You can also zoom using the slider on the Navigator palette.
To select the pixels on a particular layer, press Ctrl (Command on a Mac) and click the thumbnail of the layer. This selection will also take into account the transparency of any pixels, so painting in the selection will recreate the transparency settings of the original layer. The example at the top of the next page shows a selection I made based on one of the text layers in my sunset document.
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