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)

SAP FICO Reference Books:
SAP Financial and Controlling Interview Questions, Certification and Configuration, Books

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SAP Controlling

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SAP FI (Financial Accounting) Configuration Hints and Tips

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SAP ABAP/4 Programming, Basis Administration, Configuration Hints and Tips