Your cash payment into the S-Corp is considered a Contribution, which increases your equity. This transaction does not affect Retained Earnings.
Report this under Business Info >> Partner/Member Information. Edit the member info, and continue through the interview until you come to the Capital Summary page. Enter the amount you paid into the company as a Cash Contribution.
However, the loss you experienced this year will reduce Retained Earnings. This will be recorded automatically from your entries for income and expenses.
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