I wrote a manual payroll check to an employee who's check was accidentally left out of the payroll processing. (we use ARMI). What account should I have written the manual check against? (I put it under prepaid expenses), and how do I reconcile it with the payroll reports from Armi so that taxes and such are correct?

I expect you might use a payroll clearing account to make payments then allocate the costs, however having done what you have done, you should clear the transaction from prepaid expenses to the wages allocations normally used for this employee by journal. You will have to make the appropriate entries in the payroll records.

What is not clear in your explanation is whether the payroll records are correct and the cheque was not drawn or the payment wasn't part of the payroll at all.

If the payroll records are already correct then all you have to do is make the appropriate journal. It the payroll records need to be made then make teh entries in the next payroll and rebank the funds crediting them to prepaid expenses