A preposition is a word that links a noun, pronoun, or noun phrase to some other part of the sentence.
There is no definite rule or formula for choosing a preposition so its up to you to identify the right one and how it is used.
A preposition is used to show direction, location, or time, or to introduce an object.
With
Used to indicate having something
(He was caught with a heavy bag of money)
Used to indicate being together or being involved
(I ordered a cup of coffee with my bagel)
Used to indicate using something
(I wrote this novel with only a pen)
Used to indicate feeling
(I'm filled with joy at the sound of your news)
Used to indicate agreement or understanding
(I am glad we agree with one another)
Over
Used to indicate movement from one place to another
(Please move that book over onto the bookshelf)
Used to also indicate a downward motion
(He fell over the edge of the bridge)
Used to refer to a period of time
(She stayed at my house for over six months)
Used to express more than expected amount
(He was charged ten yen over the normal price)
By
Used to indicate a mean or method
(I went to my friend's house by subway)
Used to indicate the person that does something
(The food was cooked by a professional chef)
(The television was sold by the store clerk)
Used to indicate an action with a particular purpose
(You can win the lottery by buying alot of tickets)