Hello Sreedhar,
Please find the below link to get the document on APP config and Run for your easy reference.
1. Yes, you need to configure APP for all 19 Company codes. Create the config in multiple TRs ( 5 or 6)which is very easy to trace out if any error is occurred rather than creating in a Single TR.
2. Create new payment method NEFT/RTGS by copying an existing one else create new one.
Above document will clear your doubts. Revert us for any issues.
Thanks & Regards,
Lakshmi S