I would get rid of the paper invoice entirely. If these are truly employees, they are not submitting invoices. They are just submitting claims for reimbursement. So let the expense claim in Manager be the only record. If you are using server or cloud editions, make employees enter claims themselves. (This will guarantee the are put in, because you won’t reimburse unless they are.) If using desktop (with only one user), create the expense claim from the receipts the employee gives you for whatever s/he bought. Every expense can be posted directly to the appropriate expense account. No need for all the extra steps. You can print a copy of the expense claim for the employee, if desired. Or they can print one for you and attach receipts.
Employees’ expense claims post directly to Employee clearing account, so when you pay them, you can see what you owe for expense claims.