Hi Sameer,
Your question is very likely too general to generate much response on here. You might want to specify in more detail exactly what you're trying to accomplish.
In general, you'd likely effectuate your web.config changes by just modifying them in whatever way you intend. For example, to add a new AppSetting, you would just insert the following element:
<add key="MySetting" value="MyValue" />
You retrieve these values via the System.Configuration namespace, typically using the System.Configuration.Configuration object. The AppSettings property would allow you to retrieve the aforementioned element.
Hope this helps in general. If you require more assistance, I strongly recommend restating in more detail!
Brandon