Hi Shawn F!
After you have moved the application icons, back into your Applications folder, as Allan advised, another method of installing an Alias of an application, in the Dock, is to open the Application from the applications folder, and while it is running, position the cursor over it's Dock icon, hold down on the mouse until a contextual menu appears, and select
Keep In Dock.
You're lucky you didn't empty the Trash! If you had, the apps would have been deleted!
ali b