the only way for the links to work and not show the subfolder is to move the store out of the subfolder
the links must point to the subfolder if that is where he files are.
Your friends over here at WebAssist! These Dreamweaver extensions will assist you in building unlimited, custom websites.
These out-of-the-box solutions provide you proven, tested applications that can be up and running now. Build a store, a gallery, or a web-based email solution.