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When the owner keeps funds from customer payments, you still need to process it as Sales. Then, in the Banking deposit window, you can can show "cash went to Owner Equity" and that would be a Negative (for QBO) or, for QB Desktop, it's a provided entry at the bottom of the Make Deposit screen. Please see my attachment.
I categorized a cash deposit from my bank feed as owners equity investment. It shows in that account in my chart of accounts, however, when I reconcile for that statement period it shows a discrepency of that amount. Is this amount to be posted to another account or something?