There's no way to manually choose your opponent or skip opponents, the system will detect all clans matching your clans requirements and choose one of them. So if you're lucky you'll maybe be playing against the mentioned clan, although the chance is close to zero.
If you could choose your opponents there would probably be people abusing the system and boosting (Create 2 clans, let one clan win, then the other etc.)
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
Best Answer
No, as you stated, you can only transfer your home base to war base. Not vice versa.
Source: Being in 50+ clan wars and a leader of a clan that wars non-stop.