Depo allows you to mark the pending payment as paid manually just like Shopify allows you to do that. You can use our Mark as Paid feature to do this.
To do this, head over to Depo > Orders > Manage > More Actions > Mark as Paid.
Here you can enter the details and the payment will be tracked as well as the deposit will be considered as taken.
Here is a video that can help you understand the whole process :