While your units are upgrading, your builder can be building. But which building should be upgraded first? What should be the builders priority? My first thought was to take the strategy of upgrading all Collectors and Mines as soon as possible. I soon discovered, however, that Town Hall tactics hardly translate to the Builder Base.
Elixer Collectors and Gold Mines do not need to be upgraded since you will be obtaining most of your resources through the daily battles. Which brings us to your priority when upgrading your buildings. Your greatest priority should be to upgrade your Star Laboratory. Your Star Lab will enable you to upgrade your troops while your builder is enhancing your defenses. Upgraded troops win battles; won battles are what get you resources.
Your next priority needs to be your Builder Hall. Believe it or not, the rushed base works far more effectively than in your Town Hall. This is because a rushed base gives you the opportunity to quickly lay down more defenses, walls, and Army Camps.
Finally, your priority "building" should be your Battle Machine. Getting your Battle Machine to the first level of their special ability is imperative in winning battles, and will significantly improve your percentage.
What next? I recommend reviewing the last several battles you lost. Why did you lose them? Air troops? Improve your air defense by adding the Air Bombs building or the inferno. Did you lose by a swarm of Barbarians? Focus on your Crushers or Double Canons.