I will post a link with a whole article dedicated to different clan layouts. Basically it all depends on what you're looking to do. For your purposes, not losing trophies, you'll want to center your clan castle and build up as many defenses around it as possible, to keep things away from getting your castle and instantly winning the battle, in turn killing your trophies. Here is an article explaining what different layouts are, advice on how to set your base up, and I'll even link a place where people give layouts that have worked the best for them, give them a try and see which one's work for you.
Farming Base: A base that is used if you're looking to protect and keep your loot as high as possible. If you're saving up to upgrade your TH, or something else, this will be the base for you. Potential for a lot of trophy loss here, as usually you set your TH outside so people attack it for an easy win and then leave.
Trophy Farming Base: This layout will help guard your Town Hall over anything else. It is used when you don't care as much about the loot, but more about getting as many trophies as you can get, staying high on your clan in terms of trophies. It will make it harder for people to get to your base and get that guaranteed star that comes with destroying the base.
War Base: This is usually pretty close to a Trophy Base, as it protects your Town Hall over all else. There are subcategories of these bases, such as "Hog Resistant" bases, that will protect more against attacks using Hog Riders(which are popular in wars). They usually keep the TH and Clan Castle close together, as to force the attacker to make it past some of your defenses before the clan castle is released.
CoC Layouts
CoC Layout Explanation
All defensive towers are active in your war base, even if:
- They're still being built (Level 0 to 1)
- Being upgraded (they'll be at the level before the upgrade start)
- Out of ammo (ie. X-Bows)
Answering your query about newly built towers that haven't been completed yet:
They'll function as normal, they'll be physically there (not leave any gaps) except only as Level 1.
I mean c'mon... Who's seen a Level 0 building?
Note: This only applies to newly built buildings... Or at least those that are under construction.
Cancellation of its construction will remove the building from your War base.
Best Answer
After Preparation Day your Clan War Base is locked to the arrangement and highest completed upgrades
Source: Clash of Clans Wikia - War: The War Map (2nd question) * emphasis mine
However it has came to my attention that the Wikia may be out of date as there was an update to the game that allowed you to have separate layouts however i so still believe the parts i emphasized still apply
as such any upgrades done after Preparation Day wont be applied to your Clan War Base until your next war. they will however still apply to your regular base