Wages:
Have you registered all the employees of the company with Revenue, and have appropriate tax credits?
Actual wages calculations would depend on earnings to date, and individual tax credits allocated.
Proprietary directors are seen as self-employed. They pay Class S Prsi, and the company does not have to pay Employer's Prsi. (which is not always 10.75%, it's 8.5% where earnings are €365 per week, or below)
For next year I'd advise Collsoft Payroll, could even be worth it for this year, something like €140 plus vat.
Expenses:
Civil service rates, or lower, can be paid tax-free- keep all records. A "round sum" or higher rate and you're talking taxable. Or you can just refund all actual expenses.
I would take it that the civil service rate covers petrol, tax, repairs etc, but tolls and parking would not be included. Refund separately.
Good luck.