banking

Is it actually a "paycheck" done through your Payroll system or just a payment?

It sound like you should be making an Owner's Equity payment.  NOTE: Pending if there are multiple owners and if this is a Sub S, Sole Proprietor, etc. there may be a specific way this needs to be done, so you should check with your Tax Accountant.  But the following will let you make the entries and it should be changeable if it needs to be done a different way.

There should already be an Owner Equity Acct in the Chart of Accounts, it might be Inactive/Hidden, but odds are it is there.  If not, just create a new Equity Account and call it Owner Equity.  I would also suggest creating two Sub Acct: Owner Draw and Owner Contribution.  These are not mandatory, but it can make things easier when you're looking for a payment or running a report.

The Check/Payments made to the Owner would be associated to the Owner Draw Acct.  If the Owner puts money back into the Company, it would go to the Owner Contribution Acct.  Do not worry about +/- balance in the accounts.  They to show the flow of money and the CPA/Tax Accountant is really the only one that will be looking at them.