What you're seeing in the Dock are essentially Aliases of your apps so if you've replaced your application icon, you need to drag the old icon out of the Dock (so it vanishes in a little puff of smoke) and drag in the new one into the Dock from your apps folder.
If you want to change icons find the app in your apps foleder select it hit command I and with your new icon If you have one hit command I then Copy the icon on to the icon of the app.