The 'Deposit Threshold' feature can be found in Settings > Invoices, Estimates & Receipts.
Note: This feature is for Enterprise users only
At the top of this modal, you can choose whether you want this threshold applied for all customers, no customers, or using the setting determined in the customer profile. From here you can set your threshold, and if you want the customer to pay a set dollar amount fee or a percentage of the estimate total.
This is what the customer-specific setting looks like in their customer profile