You can configure this through transaction code OBXR or by following path;
SPRO > Financial Accounting > Accounts Receivable and Accounts Payable > Business Transactions > Down Payment Received > Define reconciliation account for customer down payment
If you configure this then down payment will automatically be made to this account instead to the reconciliation A/C.
Now double click on Down payment line
Update your chart of account
Against your reconciliation account you need to mention the special general ledger A/C.
Now save it and click on properties to have a look on the configuration.
How to define alternative reconciliation account for Down payment made to vendors
You can configure this through transaction code OBYR or by following the below path;
SPRO > Financial Accounting > Accounts Receivable and Accounts Payable > Business Transactions > Down Payment Made > Define reconciliation account for down payments
Now double click on down payment for current assets and enter your chart of accounts.
Against your reconciliation account you have to enter the special general ledger account and save it.
How to configure vendor down payment request for automatic payment program
To configure for automatic payment program you need to double click on payment request F. After entering your chart of accounts you need to assign the special general ledger account against the reconciliation account.