If an invoice already exists for a given charge or payment, perhaps thanks to a recurring invoice, DoubleAgent will use it. But if no such invoice exists, DoubleAgent will create a suitable one.
When it comes to numbering the invoices, FreeAgent supports global invoice sequences, per-contact invoice sequences, and per-project invoice sequences.
DoubleAgent offers you another alternative: your invoices can use a custom sequence specifically for your Stripe or GoCardless integration(s). This is particularly useful when your customers are paying you for a product or service – all your invoices for that product or service can use the same invoice sequence. You can't achieve this with FreeeAgent alone.
For example, let's say you offer a product called My Super Product and your customers pay for it via Stripe or GoCardless. You can have all the invoices generated by DoubleAgent automatically number themselves MySuperProduct001, MySuperProduct002, MySuperProduct003, and so on.
The idea for this came from one of our customers – thank you!