Taking a deposit is done by taking a payment on account. This applies a credit to the client's account to be used at a later date (or refunded).
Taking payment on account
Click on POS in the right hand menu.
Search and select the client in the search field at the top left of the screen.
Click "ACCOUNT" in the "Add invoice item" box.
Enter the amount, who is processing the payment (Sold By) and then click "add item".
The account payment will appear as a line item in the invoice.
Take payment in the usual way by selecting a payment method via the blue buttons on the right of the screen.
Once complete, the account payment is recorded in the client card / financials / account tab.
When the client wishes to use the account balance against a future invoice, use the "Account" blue button as the payment method for that invoice. If this amount is not enough to cover the entire invoice, use an additional payment method in the usual way.