Define more than one reconciliation account for one customer or vendor in fi

Here you can define the alternative reconciliation in front of that reconciliation account which you define in the Customer Master Data :-

For setting in FI :-

IMG -> Financial Accounting ->Accounts Recievable and Accounts Payable -> Business Transaction -> Postings with alternative reconciliation account ->Define Alternative Reconciliation Account for Customers or Vendors -> Double Click on the Line Item

For setting in SD :-

1. IMG -> Sales and Distribution -> Basic Function -> Account Assignment/Costing -> Reconciliation Account determination
-> Define Access Sequence
(This is used to define based on what criteria the system will propose an alternative customer GL reconciliation account)

2. IMG -> Sales and Distribution -> Basic Function -> Account Assignment/Costing -> Reconciliation Account determination
-> Assign GL Accounts
(This is the Alternative GL account assignment, which will override the reconciliation GL account in customer master)