Hello,
If you are facing only problem with ConnectionString for both application so you can define more than one connectionString in one config file. I don't think that you need to use more than one config file for both.
Please refer this
http://msdn.microsoft.com/en-us/library/ms254494.aspx[
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example:
<connectionStrings>
<add name="connection1" connectionString="user id=user;password=123;server=10.0.0.1;database=myDatabase;connection timeout=30"/>
<add name="connection2" connectionString="user id=user;password=123;server=10.0.0.2;database=myDatabase;connection timeout=30"/>
</connectionStrings>