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Bank deposits coming from multiple sources

Is there a way to enter bank deposits that consist of customer payments AND owner investments or receivables from non-customers (such as loans from vendors, owner investments, etc.) so that the bank deposit is accurate?

How do you record a deposit for credit cards where the merchant fee is deducted from the deposit?

When payments are received, I always enter those payments into an "Undeposited Funds" account (for myself as well as for the majority of my clients). When the client finally makes bank deposits, how do I record the bank deposit from Undeposited Funds account to the correct bank account? The only entry showing for making the deposit is the Undeposited Funds account.