Geeting reference to a site

This is quite straight forward

using(SPSite mySite = new SPSite(http://mysite))
{
using(SPWeb myWeb = mySite.OpenWeb())
{
}
}

How to customize your SharePoint site?

All teplates are in 12\TEMPLATE\SiteTemplates. New templates can be developed inside 12\TEMPLATE\SiteTemplates. For more details click here