Dear Soumya,
For bank reconciliation purpose and the bank payment and received we need to create three account(GL). One is main bank account, One is for making payment and one is for Received payment. Ex: 350000 is main bank,350001is for receipt &350002 is for payment .
When you will transfer form bank to bank through any of the T-code take 350002 to credit the bank and .350001 is for Debit the bank. you can do manually through FF67.
If any clarification please feel free to speak.
Regards,
Shyam