When an automatic (recurring) invoice is generated, I would expect it to not only sweep up all of the billable items, but also grab any available deposits on the account and apply them to the invoice. Alternatively allow the client to add deposits when paying (though this one has limited usefulness, as the invoice would be auto-pay most of the time). If needed, a toggle could be useful -- something like "Include/apply available credits/deposits". Without these options, recurring invoice flow is incompatible with deposits, which can happen for various reasons, not just for starting a new client and taking a "security deposit". Deposits can occur throughout an established client relationship, and should be compatible with automated billing.