I'm not sure if my war base is attacked, or my village layout. If it is my war base, I can make my village neater. If it is my village layout, no wonder I've been getting recked.
The base that is normally attacked by other players around the globe in multiplayer is the Home Village. Players in the clan war cannot attack this base, unless they somehow manage to come across it in normal multiplayer (of which the chance is very, very, very small and essentially impossible).
Your War Base is only ever attacked by people on the opposite team of your clan war. It cannot be attacked by players in normal multiplayer.
How do you know which was attacked? All attacks on your Home Village appear in the defense log of your inbox. Attacks on your war base only show up in the war screen.