At the I-829 stage, USCIS wants to determine that the investment has been made and used for the business activities that were originally stated at the I-526 stage, and that the jobs are being created. Employment records are helpful, as are any contracts that may be in place for the services. Having a parent/subsidiary relationship among the various entities could help in getting all jobs counted, but it would be beneficial to you to retain EB5 counsel to review your structure.
The questions you ask are very thought provoking. You need to retain the services of both an experienced EB-5 attorney and economist. The Regional Center will have to file with the USCIS an annual report on its project activities including number of investors through the I-924A application. The I-829 in respect to a Regional center project will file the Economic Report showing how indirect jobs were created. In a Direct EB-5 project at the I-829 stage there will be a need to provide more detailed information on each of the employees to show they were full time and either US citizens or Permanent residents.