all your textures sould be in the mcp/src/minecraft/assets/modname/blocks(items, whatever)/
so you create assets folder inside the mcp/src/minecraft/
After reobfuscating the game, you copy the assets folder from src/minecraft inside your .zip file.
If you are not sure about the paths, check the Eclipse console. When game launches it tries to load all the icons. If the icon is missing it is going to display a message like this in the console:
Using missing texture, unable to load: somemod:textures/blocks/someblock.png
That way you can determine if you have your textures in the right place.