Do we still track damage on indestructible creatures?
Creatures with indestructible can take damage like normal, and will still be counted as having that damage for anything that cares about that.

The full definition of Indestructible is:


  702.12. Indestructible
  
  
    702.12a Indestructible is a static ability.
    
    702.12b A permanent with indestructible can't be destroyed. Such permanents aren't destroyed by lethal damage, and they ignore the state-based action that checks for lethal damage (see rule 704.5g).
  


It does not prevent damage, so it takes damage like normal.