In order to keep your inventory updated you need to first turn on Enable stock management then go to Settings > Product > Inventory.

Next, turn on Enable stock management at the product level and set the desired stock level in the Stock Quantity section.

Once you set the stock level WooCommerce will deduct from this amount, every time you make a sale, and it will also simply adapt to the quantity of the products to low or out of stock as necessary.

Every time you receive a shipment, you will regretfully need to go through and manually adjust the numbers. Stocks can only be increased down by WooCommerce; not up.