If you are truly one company with different offices, then you only have one EIN (Federal Employer Identification Number).
You would make one payment covering all payroll for the federal items- Federal W/H and FICA/Medicare(both employee and employer). When the time comes you will also make one payment for Federal Unemployment taxes (FUTA).
You did not state where the offices are located however. If they are in different states, then you will have to handle each state separately for income tax withholding and state unemployment as appropriate. You also may have some local tax issues.
QuickBooks should have been setup prior to running this payroll and it should handle most, if not all, of these issues as well as any deductions for insurance, pension, etc.
Your internal accounting may be a different matter. If you are trying to have Income Statements for each office, then you will need to allocate the gross pay and employer expenses to the various offices.
Hope this helps.