How do I generate separate GST returns for each branch or sub-company?

You can only generate separate gst returns for each branch if you are using BUSY enterprise model and have enabled multi branch feature in that company
 Find out the steps to maintain multi branches in one company
 Step 1 : First go to administration
 Step 2 : Then go to configuration 
 Step 3 : Then go to features and option 
 Step 4 : Then go to enterprise features
 Step 5 : Then enable multi branch details option
 Step 6 : Then create new Branch master and enable create voucher series group , user and material center for that Branch if required
 Step 7 : Then mention Branch info details 
 Step 8 : Then configure branch options
 Step 9 : Then mention branch state and tag that voucher series group of branch 
 Step 10 : Configure gst details of that branch
 Step 11 : Then go to administration
 Step 12 : Then go to users
 Step 13 : Then tag that branch in those users which is related to that branch
 Step 14 : Now you can log in that company with branch user 
 Step 15 : Then go to display 
 Step 16 : Then go to Gst reports
 Step 17 : Then go to Gst returns
 Step 18 : Then go to gstr1 e return option
 Step 19 : Then select the format to generate return through json ,csv, excel or can direct upload also gstr1 for that branch
 Step 20 : And upload that file to GST portal