Could you provide more information…
1. What is the business of the company?
2. Is he a lawyer?
3. Was there an actual contract?
4. Is he always writing the same amount on the check, with a pattern?
5. Is your boss a partner or the owner of the company?
I think what you first needs to rule out is 1) if the withdrawal is legit, and 2) if there's actually a contract. Obviously, if he's a partner or an owner, it will be reasonable. I would also back track if there's an actual contract, even a verbal one. This might be back ages.
I've worked with a small private company, where my boss is the COO but also acted as the lawyer of the company and the lawyer of the owner. He has a fix payroll from the company, but would also get contracted money for his esquire services. His payroll is reported on the books, but instead of getting paychecks, he will write himself in regular checks. And then he would also write himself the esquire service checks. His name and then his signature. In addition to this, he does borrow short loans from the company, to maintain some sort of operations and/or used it as an escort (or something). He does sometimes back it back, but doesn't follow a pattern.
What I usually do to record his money is first separate the esquire services and everything else. Then on that “everything else” I wrote it all as loan. I would at the end of the year write-off the loan that's equal to his portion of the payroll, then minus what he paid back, and then figures out where the rest of money is.
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I would say the degree if it bothers you, will depends if you are certifying the books and presenting it to the bank or whatever it might be. In my case, I am only in charge of the bookkeeping portion. There's another CPA who will certify the book. The partner is also aware of the situation. I have no obligation or responsibility.
Have I ever see any contract on his esquire services? Never. It's probably a 20 years old deal. I did flip back the book 7 years past history and every year it was about the same, it probably just existed.
This type of things happens a lot with lawyers, royalties, and extremely small owned companies.
New York - NYC
Passed CPA Exam (11/2014)
In search for a position in NYC that will fulfills the license requirement.