Adding stock to an SKU is done by creating a goods-in notification for one of your warehouses called an "Inbound Stock Notification".
Click "Create Inbound Stock Notification" on the "Stock" tab on the format page
Select warehouse that will receive the stock
Set an expected arrival date
Set quantity per item ordered
Optionally add several products per ship notice
If you allow items to be pre-sold, they will be available for customers to buy immediately, and the orders will be fulfilled when the stock has arrived at the warehouse.
When the goods itemised in the Inbound Stock Notification are received; any differences in stock quantity will automatically be updated to your stock levels.