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1. Whom should I pay the money?
2. To whom I have to pay the money?
3. Who should I pay the money?
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Who should I pay the money to?
Who do I have to pay the money to?

To whom should I pay the money?
To whom do I have to pay the money?

The third and fourth are rather formal.
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Short and simple and natural:

Who do I pay?

CJ

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To whom should I pay the money?

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To whom I have to pay the money?

 CalifJim's reply was promoted to an answer.