Hi Chatchawal,
Please subject it to tax and SS if you believe that it is the correct process. Is the employee's SS contribution has not yet reached the maximum last month?
Does your system has no ability to charge the specific income to different cost center? The tax incurred for this retro income can be charged to his current cost center if you're system could not be able to breakdown the tax to the two cost centers. I think, the important thing is to charge those income to the cost center provided by client.
The retro income is for June 1-5, 2016. The EE is hired last June 6, 2016 thus the income paid last month to him is for June 6-30, 2016.
I hope this makes sense.
Thanks,