Do I need to seperate deposits and withdrawals from staking apps?

I deposited $4,750 PYUSD into a staking app. I withdrew $4,761 PYUSD making $11 PYUSD reward.

What do I need to change so I see this $11 reward and am not taxed on the whole deposit.

You should tag your staking transactions and add a deposit tagged as reward into the Pool wallet. This is explained in the article below:

Staking and farming tokens