How should organizations record the payment transactions made with a controlled entity on 990-EZ?
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If an organization has engaged in a transaction with a controlled entity, and if the transaction value exceeded $50,000, then they are supposed to file Form 990 instead of 990-EZ and must attach Schedule R along with the information return.
 
A controlled entity is an organization described under section 512(b)(13) which may be a stock or nonstock corporation, association, partnership, LLC, or trust of which the controlling organization owns more than 50% of:

• The stock of a corporation (measured by voting power or value)
• The profits or capital interest in a partnership, or
• The beneficial interest in a trust or other entity.