When adding a namespace, I’ve found I also need the assembly. If your assembly is also myApplication do this in web.config:
<add tagPrefix="one" namespace="myApplication.Controls" assembly="myApplication"/>
Then, just clean and rebuild and it should all work. Once this is in your web.config, you don’t need to add it to your page unless you’re using this in a control in the same directory, then you’ll need the reference at the top of the web form. But, I recommend against using custom server controls in the same directory as user controls.