Yes you can use multiple databases in a single application. This can be achieved by updating your connection string where in a same server or different server you can replace /add the database name or server name based on your requirement.
Suppose in your config file you have a connection string
<add name="DefectConnection">
connectionString="Data Source=SERVERNAME; Trusted_Connection=true;" providerName="System.Data.SqlClient"
/></add>
At run time you want to add the database name. So add Initial Catalog within your code as below:
protected const string ConnectionStringKey = "DefaultConnection";
static string preConString = ConfigurationManager.ConnectionStrings[ConnectionStringKey].ConnectionString;
private static string conString = String.Format("{0};Initial Catalog={1}", preConString, "YOUR DATABASENAME");
Here you can use the configuration settings to get the connection name, you will be able to change the database name with the database name that you want to use.
You can use them within any place within your code.
Also you can use multiple connection strings as well.
Hope this will help.