In your bank deposits journal you would add the new posting in the transaction explorer with your bank account specified and in the details of this transaction add the two entries to:

Your Customer AR account 10,000.00
Your Hold Back Account (1,000.00)

Block the posting above and right mouse click Tools > Apply Deposits.

Press F11 in the Cr Account (or right mouse click Window > Define Column) and alter the pick root if the accounts being displayed with F3 (pick) does not show your Hold Back Account.