Your post is very vague and unclear about who is paying whom for what, what the activity of the nonprofit organization is, what merchandise is being purchased or sold, and by whom. But as a basic principle, you need to keep the funds and accounts for the organization completely separate from your own personal funds and accounts. If a student is paying the organization for something, that payment has to go directly from the student to the organization. If the organization is buying or selling something, those transactions have to be to or from the organization's account. Nothing should be going through your personal account.
Since you have already mingled the organization's funds with your own funds, you need to hire an accountant to straighten things out. We really can't help you with it here in this forum. The problems go way beyond what to put on your tax return. Mixing the funds of a nonprofit organization with your own funds will indeed look suspicious to the IRS, whether the amounts are large or small. You may also have violated some laws about how the funds of a nonprofit organization are handled, so you might need legal help as well.
