Phase one of clash of clans clan wars begins with preparation. Preparation day lasts 24 hours and is followed by Battle Day.
During this time your clan will prepare their defenses, gather information by scouting, and start plans of attack. By scouting your enemy you can rearrange your war base and begin donating reinforcement troops to your clan mates.
Your war base is separate from your village. It will be automatically generate based on your village layout. But you can move things around and have your village one way and your war base another. Keep in mind. After preparation day you can not rearrange your village. Your clan castle at your war base is different then your clan castle in your village. It will need its own set of troops.
Read about Clan Wars Explained | Clan Wars Battle Day