expense allocation using payroll reimbursement

Using a check to vendor, after the fact record the expense and negative reimbursement account so that check is zero. Or do similar in a depisit where expense will be negative and reimbursement positive.. You can do same in a journal entry though names of line items will not track by vendor. Debit expense, credit reimbursement

I had the same question and what I did was adjust the reimbursement amount off of the reimbursement account (in chart of accounts) and add it into the applicable expense accounts. I do this once a quarter so it's not a big deal. That way I don't have to write separate cheques. The Total Pay Report gives you reimbursement totals for whatever period you select. 

That is exactly what my accountant said to do and what I did, however, the GST paid on those expenses do not show up on the GST/ITC report. That is really my question. I can run an expense report and they will be there but these expenses, which end up being company paid, are not captured for the refundable GST paid. Writing separate cheques would avoid that but then we lose a convenience of payroll.