Thanks for joining this conversation, @jasontrout.
You can create a journal entry to transfer the remaining balance from the security deposit to bank account. Before we proceed with the steps, I highly suggest consulting an accountant or accounting professional for guidance on which account receives the debit and credit side of the transaction.
1. On your QuickBooks company file, go to the Company menu at the top.
2. Pick Make General Journal Entries on the drop-down.
3. Enter a Date. The Entry No. should automatically populate.
4. Enter the necessary details, then hit Save& Close once done.
For additional information, check out this article: Record a journal entry.
That should point you in the right track. Please let me know everything goes. I'll be here if you need further assistance. Take care and have a great day.