Dear Soumya,
You can make the transaction through f-02.
I will give a simple example I hope it will helpful to you:
Ex: we have two bank AXIS & SBI. We have to transfer from AXIS TO SBI Rs.1000/-
Steps:1.make a One time Vendor :SBI Bank
2.Make one time Customer: AXIS Bank.
Make the link in Vendor/Customer master data.
3.Make payment :SBI(One time vendor) a/c Dr 1000
TO 350002 a/c Cr 1000
4.Receipt 350001 a/c Dr 1000
AXIS(one time Customer) a/c Cr 1000
Now you can do the bank reconciliation in the same way as you are doing in past for incoming and outgoing payment.
Regards,
Shyam