I would file the CTR, personally. The individuals came in with cash that, through the course of the transactions, ended up in the business account.
I'd treat this similarly to the idea that some people come in with cash, deposit the cash, then do a debit to create a cashier's check. If the cash was between $3,000-$10,000, you would still complete a Monetary Instrument Log on the purchase.
I would complete a section on the Business ($10,759.00 cash in)
A section on employee ($4,759.00)
A section on business owner ($6,000).
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