In Stock Manager you have two options which you can select via the tab towards the top of the page:
In Stocktake you can overwrite the existing stock quantity with a new one. It's typically used during a stocktake when you want to overwrite existing quantities.
The stocktake screen monitors ongoing stock changes in the background eg if a new order is placed and will alert you when quantities have changed so you can decide if the New Stock Quantity needs amending before you apply the changes.
Stock In / Out Adjustments
Stock Adjustments don't overwrite but add / subtract (plus / minus). This is ideal for busy shops where you don't want to overwrite existing quantities but need to make adjustments. A typical scenario would be adding incoming stock from your supplier or writing off damaged stock. As stock is added / subtracted at time of applying the changes it's safe to use in busy shops and does not overwrite any changes made eg when a new order is placed.
The "estimated new stock quantity" shows the likely new stock quantiy once your adjustments are taken into account. However as the actual stock adjustment is made when you apply changes, the actual new stock quantity may differ.
Scenario: Product A has a stock of 5 items. You adjust with 10 new items as you've just got a delivery from your supplier. Estimated new stock is 15. But just before you click to apply the changes, a new order for 1 item comes in. The actual new stock is therefore 14 which is calculated as 5 - 1 + 10 = 14.
The adjustment screens monitors ongoing stock changes and will alert you when stock changes. However as you are adding / subtracting stock, these changes don't pose any problems. When stock changes, the new quantity is shown with an alert symbol, and the estimated new stock quantity is adjusted.