Not being an eBay seller myself I don’t know how much detail you can download from them in CSV format - if you can get something that gives you a line for each sale with the date, amount (gross at least, possibly VAT too) and payment type then you should be able to massage that in Excel or similar into a suitable form for the invoice import tool. This would let you create one invoice in QuickFile per sale on eBay, but it’s probably simplest to keep them all against one dummy client name like “eBay sales” - you can always switch a given invoice to a “real” client name if they (the buyer) were to ask you for proper VAT documentation.
I guess you’d just do this in bulk once a week or so.