You can't just change the icon in the dock or stack, you have to change the icon on the application itself (Get info - CMD-I - on the app, copy/paste the new icon over the old one). Once you've changed the icon it will also change in the dock and stacks, although you may have to log out and back in first.
To stop NeoOffice from auto starting go to the accounts prefpane and delete it from login items (the checkmark on the contextual menu is just a quick way of adding an app to that dialog).