Not only can you create specific prices for a given product using Store Commander's multistore management features but you can also setup redued prices on products for specific stores.
Please refer to this article to create specific prices on products.
In the multistore management version, the grid 'Specific Prices' displays a column entitled 'Shop' and another column called 'Shop group'.
This allows you to choose on which store or group of stores you wish to apply specific prices.
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