Alliance War is a team effort, so you should consider your defense to be a team effort as well. So how should your alliance set their defense teams?
Easy! Just set them the same as your personal raid defense!
Not so fast! Alliance War in Empires and Puzzles is different than normal raids because you can only use a hero a single time. You, then, use 30 heroes in your attacks, depleting your best offense against a specific defense (if you didn't know that, maybe read about how Alliance War works here). In normal raids, if you fought the same exact team over and over again, you'd just create your perfect team and attack! But in Alliance War, after your first attack, you won't have access to those heroes again.
This is where coordinated tanks comes in. Your defense tank (the middle guy) is the most important hero on your team. It will take the most gem damage, so making sure it survives as long as possible increases your chance to successfully defend (for more information on good personal raid defenses, go here). When you coordinate tanks (the easiest example of this is to set all tanks to the same color) if gives the tanks extra longevity. Typically when attacking in a raid, you want to have a few more guys of the strong color against that tank. When you coordinate, the attackers lose their strong teams against your defense.
If you think about it from the attacker's viewpoint, they look at your defense and build their offensive team to give them the best chance at winning. If each team is separate, they can keep looking for good options to attack. If everyone is basically the same, it takes those options away from the attackers. Sure, their first team will be solid, but they will keep getting weaker each attack because those teams that are strong against that specific defense will not have a target.
So just set the tank to the same color and you're done?
Well, there are other ways to coordinate. You have to think like an attacker. When you raid, you're (hopefully) changing up your team to best attack their defenses. Sometimes you take dispellers. Sometimes you take extra healers. Sometimes you take a hero that removes ailments. Each of these attack team builds is something you should consider coordinating (usually in addition to same color tanks). Optimum would be to have one player create their perfect team then everyone else perfectly emulate that, but that's close to impossible. Instead, talk to your teammates and see what will work best for everyone. Survey personal defenses. If half of the people have red tanks, maybe that's the direction to go.
Keep applying this principle of removing options from those attacking you. Same color flanks and wings help. Everyone using Spirit Link or Counterattack (but not together!) can help. You just have to weigh the coordination with what your members have. It's not about individual strength, but rather how the teams work together as a whole.
I hope that helps give you direction for your war defense! Good luck out there!