Define 2 connection strings in your web.config file for the different database servers.
<connectionStrings>
<add name="connString1" connectionString=..../>
<add name="connString2" connectionString=..../>
</connectionStrings>
Use corresponding connection string in your application like this:
String connString1 = ConfigurationManager.ConnectionStrings["connString1"].ToString();
String connString2 = ConfigurationManager.ConnectionStrings["connString2"].ToString();
Hope it helps!!!