You can mark holding deposit as paid if applicants have paid it to you directly. To do so:

1. Open Tenancy Overview page
2. In "Holding deposit" stage of the tenancy, click 3 dots button (...) (Please note: this will be available only once the lead tenant has signed the holding deposit explained document)
3. Select "Mark as paid"

This will set holding deposit as paid and if all tenants have signed the holding deposit explained document - complete the Holding deposit stage.