If you've added a new building to your village and you can't find it in your War Base, it sounds like you probably haven't taken that building out of the war base inventory yet.

As a rule, your War Base will contain the same buildings as your regular village. However, every time you add a new building to your village, you have to go to your War Base inventory to "deploy" that building during Preparation Day and save your War Base layout. The game will not choose a random spot in your War Base for any new buildings -- you get to decide where everything goes. If you leave a new building in your War Base inventory, it won't appear in the Base during Battle Day.

The only exception to this rule is if you have never used your War Base edit mode and saved your layout. If that's the case, your War Base's layout will continue to mirror whatever you have in your regular village.