A count starts by opening a new one from the Stock Count screen. For as long as the count is open, stock balances do not change; the quantities you enter are held separately. That is what lets you keep selling while the count is under way.
The person counting types a product code or scans a barcode and enters the quantity; every line is saved as it is entered. If the same product is counted a second time, the quantity is added on top, because a warehouse is usually counted shelf by shelf and by more than one person. The person counting cannot see the system quantity. This is deliberate: someone who can see the number on the screen tends to confirm it rather than count.
Seeing the differences and closing the count require a separate permission. Show Differences puts the system quantity, the counted quantity and the difference side by side. When you close the count, the difference is posted as a stock movement with a count adjustment reason, and the count can no longer be changed. For products tracked by batch, the batch number is required.