You can deposit the money in two ways.

1. From the Banking menu->Make Deposit or
2. While receiving payments from your customer using Receive Payments in Customer menu.

i) To deposit an amount in a bank, select Banking->Make deposit.
ii) Fill all the details.
iii) Choose an account from where you are taking the money for deposit in the Deposit from the account field. For example., if you are making deposit from your investment account then select "Investment" option in the Deposit from field.
iv) If you received the depositing funds from your vendor or customer, then select customer or vendor in "Received From" field or else it is optional.