To preserve (food) by canning, freezing, drying, etc.
Our family has been putting food by for generations.
To save (money).
I have put a few hundred pounds by for a rainy day.
To perform an action without attracting the attention of.
I managed to put that transaction by accounts payable.
Of a ship: to be run aground intentionally to avoid a collision
The Bow Spring put by to avoid colliding with the Manzanillo II.