To mark an order as shipped, go to the shipment it is a part of and click on shipped

You could also mark an order as shipped from the order page, by selecting mark as shipped from the 'Mark as' dropdown.

When you mark the orders from channels such as eBay, Amazon, Magento, Shopify and Zepo as Shipped on Browntape, the same is updated to the channels. Marking orders as shipped currently does not work on Shopclues, Tradus, Rediff and Flipkart; however, Browntape is constantly working on bringing in these features as well.