i have two questions
1. should i use grass knot or ice beam on a sub petaya empoleon
2. what is a good counter for a zapdos running hp grass?
1. It depends on what your team needs coverage against, Ice beam is the obvious choice for dragons, and Grass Knot helps against bulky grounds and waters. You'll have to decide what's best for your team.
2. Any decent special wall like Blissey or Snorlax generally handles Zapdos well, and pokemon with a resistance to Electric attacks can come in on Zapdos as well. Latias resists both Thunderbolt and HP Grass, and Tyranitar can take HP Grass relatively easily with its high special defense. There are plenty of others, just make sure you predict correctly and know what you're switching in to.