Now you have to choose two options as show in fig below :
Item with respective warehouse QTY
Item without warehouse QTY
The first option i.e. 'Item with respective warehouse QTY' is for adding the item with considering the warehouse. In this when you download the sample file you will find column such as 'warehouse 1' , 'warehouse 2' etc, In which you have to enter the quantity of 1st warehouse, 2nd warehouse respectively.
Please note that the addition of quantity of all the warehouse will be updated as the total Quantity, and it will over right if any other is number is assigned to the qty field.
In the second Option i.e. 'Item without warehouse QTY' the warehouse is not being considered. You will have to just update the total quantity irrespective of the warehouse quantity.