If during adding a new product you have selected the option to include the new product in Trackable Inventory....
...and hit Save, you'll have an option to edit the product's quantity in your stock.
Just click Edit Stock Level...
...enter the New Stock Level (current actual stock), set the Minimum Stock Level and Maximum Stock Level, and then hit Update.
Optionally, when adding stock quantity, you can create a Purchase Order for the items that are being added.
Just got to the Purchase Stock section on the same panel, add a Supplier and the desired Quantity.
The Value, Account, Tax Rate and the Total amount will be pulled through automatically.
When you're sure that everything's correct, click Submit. This will generate a Draft Purchase. To convert this to a Purchase Order, see Converting a draft to a purchase order.
After updating the stock quantity, it will be shown next to the product in the Inventory list.
From now on every time when committing an invoice with the stock product, the invoiced quantity will be subtracted from the total.
Also whenever you add it to a purchase, the On Order count will increase, and once the purchase is marked as received, the stock level is updated.
To add an already existing product to the inventory, simply select it from the Products list:
On the product details page, tick the Trackable Inventory checkbox and click Save:
Then follow exactly as with adding new products to the stock including updating quantity and optional creation of a purchase order