Vておく indicates that one does something in advanced for a certain purpose or future convenience. It is also used to indicate that one leaves the present state of something as it is. On the other hand, Vないでおく indicates that an action which might usually takes place is not performed and left undone for some reason or purpose.
I arranged flowers in the room because my friends are coming.
I bought a new bag for the trip.
There will be a party tonight, so let's not eat too much for lunch.