The standard folder layout has three folders inside of data, and the .bsa files contain most of the game data such as sound, meshes, and textures. You should try to apply a mod that alters a texture so that you can visualize how to make mods of the files in these archives. Also, there is a tool that allows you to view and selectively extract from the .bsa format, it is hosted at fallout 3 nexus.
Do not worry, it is the normal structure, and mods should work in Steam as in retail. (at least any mods that we can make now, when scripts are made possible it may become a problem)