A Merchant Id means a link to the Bank/Merchant Facility. It is like one username/password. Organizations would have multiple merchant id's if they have multiple different bank accounts.
For each Merchant Id, they would need an account with their bank, plus they would need it setup with Windcave (for example). Some organizations might have a Payments2Us Tab "Merchant Facility" multiple times, but using the same payment gateway username/password (Merchant Id). This is for a number of reasons – e.g. some forms have tax and others don't.
You can create multiple Merchant Facility and Payment forms for the same Merchant Id .