If let's say a 3/3 indestructible creature takes 2 combat damage and then 2nd main gets a -1/-1, does the creature die?
Am assuming no since its still technically a 2/2 indestructible with 2 damage on it and NOT a 3/1 indestructible with a -1/-1
It does not.
An indestructible creature will die from having 0 toughness. It will not die from lethal damage (damage greater than or equal to its current toughness).
In your example, you have indestructible 2/2 (because of a -1/-1 counter), and it has 2 damage marked. It has taken lethal damage (as it has 2 toughness and 2 damage), but has toughness greater than 0, so it does not die.