Once you have picked an item for a customer order in IMERCHANT, you should open the order in IMERCHANT and check the PICKED checkbox (PRODUCT TAB).

Only check the picked button if all QTY of that item have been picked.

This will mark the item as PICKED in IMERCHANT reports. 

Try early morning order picking to get the online orders off the shelves.  

Once you have picked all of the items for an order, use the Customer Order Wrapper to group the items together and for completing the sale in POS.