The option to manually Mark Paid (or Mark Sold / Paid) only needs to be used in the following circumstances:
1) The item shows in SellerVantage as Sold / Unpaid, and the buyer has paid you through some method other than eBay. In this case, click Mark Paid and select eBay as the selling channel. If the item shows as Sold / Unpaid and the buyer has not contacted you after some time (a few days, a week perhaps), we recommend contacting the buyer to confirm that they are planning on paying, and if not, returning the item to Queue.
2) The item is sold face-to-face in your brick & mortar store. In this case, click Mark Sold / Paid and select In-store as the selling channel.
3) The item is sold via craigslist. This often means it was sold face-to-face In this case, click Mark Sold / Paid and select Craigslist as the selling channel.
NOTE: Use of the Mark Paid (Mark Sold / Paid) functionality in other cases will often cause an over sale message to appear. While this can be safely ignored under these circumstances, we recommend you follow these procedures exactly to ensure that your inventory counts are accurate and that there are no issues with real over sales.
In most cases other than the ones mentioned above, the proper action for an item sold on one of the main selling agents (eBay, Amazon, Craigslist or SellerVantage storefront) is to wait for SellerVantage to finish the sale payment.