In the early stages of my builder base, I would often experiment with the different units provided. It was interesting to see how they all worked together. One of the interesting things I discovered is that during the first four builder hall levels, you can be fairly successful almost exclusively using giants. During later levels, however, this is not as successful. As such, it becomes necessary to know which units to upgrade and which units to ignore.
Always upgrade your Giants. These troops are your best damage sponges. The more damage they are able to take, the more time your other troops (particularly your ranged troops) have to deal damage without fear of being destroyed. Giants are versatile and can work to support your Archers, Canon Carts, and Night Witches.
Archers need to be your next priority. Their ability to avoid damage for the first few seconds of deployment is invaluable to taking out buildings. Archers are excellent especially when your foe has built their defensive buildings very close to the edge of their base.
Minions are a fantastic way to swarm the enemy. Upgrading your minions is less about their power, and more about adding extra quantities to your arsenal. There are only two defenses that cause splash damage in the air: the Roaster and Air Bombs. All other air defenses must pick their targets one at a time causing a base to be vulnerable to a swarm attack from the air. Minions are the perfect troop to accomplish this.
These are my suggestions for a good upgrade path. If you can upgrade these units, focus on them until you have maxed them out; then begin to take your upgrades to other troops.