you can use a 'clearing bank' to pay the payroll cheque

(since this is an advance, you'll need to calculate source deductions)

this will deal with the advance

  debit  clearing bank

  credit advance & loans

if the employee is setup as a customer, create a no-tax invoice, where the account is 'clearing bank'

and a meaningful description

  debit  ar

  credit clearing bank

and pay the invoice, with the employee's cheque

if you don't have a customer setup, when you create the invoice, use 'one-time customer'