By default Shopify does not allow taking discounts with deposits but we have created a feature in Depo, through which you can take in Deposits and also have your customers apply discount codes while making the purchases, if needed.
To set it up, head over to Depo > Settings > Scroll down to 'Allow discount codes in Deposits' > Enable the check-box and you will be good to go.
Although there are some limitations of this feature. Here is a video that will help you understand and set this up for your store:
If you still have any queries or concerns, please send us an Email at: [email protected] or schedule a call with us.