One way to do this would be to use a workflow with a loop. You have your initial process that has a form with a table of employees and their data. Pass this table over to workflow where you could you loop each row in the table to break them out. For each row, use invoke business process to start a new process that is solely designed to save the form to the repository. In this new process, take in the data from workflow for just one employee and build a form to save into that employee's repository folder. 

The final overall process would be 

1) Main process with a table of employees -> 2) WF to loop across each row of the table -> 3) For each row, pass the employee data to a new process -> 4) This new process should save one employee's data to their folder -> Repeat steps 3 and 4 for each row.