Manipulating web.config file programmatically

To modify/add a web config entry following code can be referred

// Get the SPSite object
SPSite site = new SPSite("URL");
if (site != null)
{
SPWebApplication webApp = site.WebApplication;
// Create the modification entry
SPWebConfigModification webEntry = new SPWebConfigModification("Web Config entry " ,"Entry location" );
// Add the web config entry to the collection
webApp.WebConfigModifications.Add(webEntry);
webApp.Farm.Services.GetValue().ApplyWebConfigModifications();
}

Web Config Entry could be

"SafeControl[@Assembly="MyAssembly"][@Namespace="My.Namespace"]"
+ @"[@TypeName="*"][@Safe="True"][@AllowRemoteDesigner="True"]"


Entry location could be

configuration/SharePoint/SafeControls