I work for a non-profit sports organization, running a concession stand. The executive treasurer writes a check to me personally for start-up funds for tournaments. The amounts are between $2700 and $3500. The bank takes no issue with this, as the organization has numerous checking accounts. However, I am worried that in one year's time it will look as if the organization has written over $10,000.00 to me personally. I am a paid employee, but my paychecks are not written on that same account or in that same manner (they use a check paying company). Should I have the treasurer stop doing this?
As long as the organization imposes requirements on you that you document your spending of its front money for events, there shouldn't be a problem. That documentation will show that you don't personally benefit from those payments.
Keep copies of the documentation you provide to the non-profit to account for any of the advance funds you might run through your personal account. If you haven't done so, you might consider setting up a separate account to manage those funds if it will make it easier to keep the non-profit's funds separate from your own. For whatever it's worth, no one is reporting those disbursements to the IRS, regardless of the annual total.
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As long as the organization imposes requirements on you that you document your spending of its front money for events, there shouldn't be a problem. That documentation will show that you don't personally benefit from those payments. 