Hi Glenn77,

Depends on which income you use for the 2 employee, you can go to Setup, Settings, Payroll, Linked Accounts, Incomes.  Then, link the correct incomes to the the expense account you want. 

If you have both employee using the same income but want to link to different expense account.  The easy way is to create another income under Setup, Settings, Payroll, Income.  Let the 2rd employee uses this new income.  Then, you will have 2 incomes which allow you to link to different expense accounts.

Hope this helps.