To put your entire store on sale, Create a Discount with Bold Discounts. When you get to step 15, choose the Select All Results button in the product selector rather than the Add button.
Note: We are only able to change your product prices at a rate of roughly 1000 variants per hour. This is due to a limitation of how quickly we can access Shopify's API. Visit Why does it take so long for my sale to start and stop? for more information.