In web.config, you can have two distinct (by name) connectionstring as:
<configuration>
<connectionstrings>
<add name="MyConnection1" connectionstring="Data Source=server1;Initial Catalog=db1;User ID=id1;Password=pass1;" providername="System.Data.EntityClient" />
<add name="MyConnection2" connectionstring="Data Source=server2;Initial Catalog=db2;User ID=id2;Password=pass2;" providername="System.Data.EntityClient" />
</connectionstrings>
<system.web></system.web></configuration>
In the code behind, you can fetch these two connection in two different holder as:
private static string connectionString1 = ConfigurationManager.ConnectionStrings["MyConnection1"].ToString();
private static string connectionString2 = ConfigurationManager.ConnectionStrings["MyConnection2"].ToString();
Hope, it clarify your question.