Our Stripe integration at the moment is limited to just “Stripe as a payment option”, it doesn’t have any feed or sync capabilities. Any payments collected via Stripe outside of QuickFile will need to be manually entered for now, or uploaded from a spreadsheet.
Personally I would go and just enter one bulk transaction, every week/month to represent all sales made outside of QF and log that to a single invoice (client: bulk Stripe sales).
We are doing a lot of work with Zapier at the moment, which will allow you to sync QuickFile with 100s of other 3rd party apps (Stripe Included). You can follow the Zapier thread here.