A few tips
1) Watch.
wait for your mega-gnar, then time your E, so you can initiate on the enemy team. Remember in mega you are a tank more than a bruiser. That's your job for that time.
**2) Wait. **
Don't feel like you have to constantly attack when in a poke war. Yeah gnar's Q has decent damage, but it can't activate his W through poke alone most the time, and by constantly spamming it you just force yourself over that threshold. If you pause and let your rage die down you can delay the mega to better time the transformation.
**3) Eat the pokes! ** (assuming they don't pierce)
So something i'm not sure about is exactly how the health works with the transformations. I know if you don't take damage then you lose the bonus health, but i want to say that the bonus health almost acts like a shield, so that if you gain 500 health in mega, then take 400 damage, when you return to mini-gnar you will have not effectively lost any health.
Even so! You have bonus health regen, while in mega so you brush off the hits more easily, and you are bigger target so it's harder to miss you anyway.