please refer the following link .. you can understand better from this :

http://www.tonymarston.net/php-mysql/web-site-vs-web-application.html

There are several ways to deploy the web application

1) xcopy : Copy the files and paste the files and webserver hard drive and set the folder as virtual directory.

2) Using Websetup project : Go to NewProject from the file menu, select Other Project Types that will show u the websetup project. Fallow the instructions what the websetup file gives.

3)Precompilation : It will achieve through the Publish method our project. Go to solution explorer, select the project and click on the publish link..It will opens the window that will have three checkboxes. Please select the first check box and press ok.