Our payroll manager has been caught manipulating the books and it seems may have taken money as reimbursements without authorization. With the evidence it would be difficult to disprove. Would there be enough grounds to file charges with the data entries in the payroll program?

Need to know also if I owe him for vacation accrual even though he may only break even.

Yes, this is embezzlement. What else would you call it - creative accounting? No. Payroll managers do in fact do this sort of thing every day. If the amount found is substantial may I suggest that you document everything and then call the DA's office and file charges against the payroll manager for embezzlement? It's called theft.

Only the local DA can decide if there is enough evidence to press charges, and they may want their own accountants to review all of the books.
Your choice at this point is to turn your evidence over to them.

They are the ones to have someone charged, all you can do is present them the evidence