As an employer - you would need to establish an accountable reimbursement plan.
While that is not required - it might be better to have a written policy.
You may find here Sample Accountable Expense Reimbursement Plan.
Then - you must require every employer to report back in timely manner how reimbursements are used - specifically for tools and work clothing - there must be provided receipts.
You need to inform employees about such requirements.
For those who do not have "adequate" accounting and do not provide report within a reasonable period of time - you as employer woudl be required to report that amount as taxable wages.
In this case the employee might be able to deduct his/her reimbursed expenses on schedule A.
So - that would be very important to keep "adequate" accounting.
Regarding payments - it might be more clear to pay with separate checks and no withholding
is required for such reimbursements.
Let me know if you need any help.