Loading a stock order is the correct way to add stock quantities that have arrived from a supplier. When your stock arrives from an order you have made, it will usually arrive with an invoice containing the order number, the amount that the order is worth and a breakdown of what was included with the order.
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To perform a stock take, click on 'My Business' and then on 'Retail Stock':

Click on 'Retail Options' and then on 'Load Stock Order':

You can optionally add the order / invoice number and the order / invoice total for your records. Go through the stock items on hand and specify the quantity received of each item in this order:

Once you are done, click on 'Load Order'. You will be prompted whether you are sure you wish to go ahead and load the stock order. Once confirmed, you will be given the option to capture the invoice as a business expense. This is optional.

When this is done, the stock quantities loaded in the stock order are added to the quantities you currently have on hand.
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​E.g. If you had 4 of a particular product before the stock order was loaded, and you loaded 3 in the stock order, your new quantity on hand will be 7.
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​Stock orders can be reported on by accessing the 'Retail Reports->Stock Orders Report' from the Reports menu option.