The engines do not burn for the majority of descent. You turn the engines forward and make a short burn. This reduces your velocity and causes the orbit of your ship to eventually enter the atmosphere.
Atmospheric drag is then going to provide most of your deceleration, slowing you down to terminal velocity. You then make another burn at the very end of the flight to slow down from terminal velocity and stop.
The second stage is a good example. After making a deceleration burn, it will be re-orienting so that the heat shield at the top is facing the direction of movement. It will then keep this orientation until it is safe to orient the vehicle around for landing.
You could use your engines for most of the deceleration... but it would consume a very large amount of fuel. No point in doing so when you already have atmospheric drag to do the work for you.
I didn't mean the engines were on the whole way down. But if they aren't pointing in the right direction to begin with, you need to flip the entire 70m-long stage around somewhere in the atmosphere. Even at terminal velocity it's moving pretty fast, and I doubt it will survive going sideways at 100m/s through the air, never mind that you need some thrusters that can even develop enough force to flip it around.
That animation for the second stage reentry is an animation. Recovering the second stage will be extremely difficult and, if it is ever done successfully, I don't think it'll involve doing a 180 flip in the lower atmosphere.
Atmospheric drag is then going to provide most of your deceleration, slowing you down to terminal velocity. You then make another burn at the very end of the flight to slow down from terminal velocity and stop.
The second stage is a good example. After making a deceleration burn, it will be re-orienting so that the heat shield at the top is facing the direction of movement. It will then keep this orientation until it is safe to orient the vehicle around for landing.
You could use your engines for most of the deceleration... but it would consume a very large amount of fuel. No point in doing so when you already have atmospheric drag to do the work for you.