Merchant account is not a real bank account. It is the money in transit account which can be used either with a payment gateway (in case of online payments) or with a POS terminal (in case of retail card payments)
It is used to record received payments that are collected by your payment service provider on behalf of you.
Once a payment service provider makes a payout to your bank account, this amount should be reconciled from the side of your bank account by entering an incoming payment and selecting a merchant account in the payment details.
In this case the payout amount will be credited to your bank account and deducted from your merchant account.
This step can be automated if the bank auto-reconciliation is used, by creating a predefined reconciliation rule based on the sender's IBAN or bank payment details.
Examples of Reconciliation Rules:
Braintree
Montonio
