Hi Karthik
Correct me, if im wrong in understanding u.. As per my knowledge, the workflow will only complete the Set of Tasks which we place in each steps. Normally after the workflow is completed we run the Program to which Background job is already defined. But in your case the background job has to be run automatically after the workflow is finished & also it must store the data to the particular custom tables. but i don't think so if such is the case the workflow can run/update it. Its a separate activity which u need to take help from ABAP team where they can do some program & build a logic once the workflow is finished. so, then it will be working with the workflow simultaneously.
lets see what our experts has to say on this..
Cheers
Pradyp