I would start with checking out @TheRedDelilah’s youtube channel for some great intro to hunter videos such as:
Steal Essence (Gold Hunters and up): https://www.youtube.com/watch?v=-QpgrN4Yvm0
Cloaking part 1: https://www.youtube.com/watch?v=P5rEpo3wzrc
Cloaking part 2: https://www.youtube.com/watch?v=QP7_s79N8Yk
As many have pointed out, hunters are not necessarily meant to clear out an entire base, just set it up. I have one guy on my team who is a level 150 ish with Hau, and is pretty awesome. He has posted videos to our team of taking on some level 300-500 bases with 2 dragons, setting it up with Hau by sanding the crap out of the base, then sweeping up with a level 1 ember or Spindra with enfeeble (thanks @OrcaFrost) .
Only in wars and atlas attacks does it matter to use only one of your dragons for 5 flames. And you should always ask for backup in either case so you fly a hunter to set it up, then have someone else sweep up what you missed. It really means you have to rely on your team and do some planning on a base on how to take it down at times.
For PVP events, you can use 3 dragons and it wont matter the points, hell, I usually use 3 dragons on every run to stack my inner fires.
It takes practice. And you will die a lot trying to master these skills. But in the long run it will pay off.