Can I pay an employee 1/2 their salary by payroll check & 1/2 by accounts payable check?

No you cannot do that. The form W2 must show all wages. No payments should be made through AP. Except expense reimbursements, which could be made through payroll also but are allowed to be made through AP. Many other agencies rely on payroll data for example the state unemployment department. You will also get in trouble with the IRS. There are specific rules governing this very thing.