I have a custom version of Enterprise Library on my development machine along with the Microsoft Signed Version of Enterprise Library that I downloaded from Microsoft.
The Visual Studio Integrated Configuration Editor by default will use the Microsoft Signed Version of Enterprise Library Assemblies, which by default are installed in C:\Program Files\Microsoft Enterprise Library 3.1 - May 2007.
Depending on the application, however, I may want to choose my custom Enterprise Library Assemblies ( which could be located where the source is installed by default - C:\EntLib3Src ) over the ones that are the machine default.
You can easily do this in Visual Studio by changing the Solution Properties. Change the Enterprise Library Configuration Set to be used by the Enterprise Library Configuration Editor:

Now I can choose my custom version in EntLib3Src and the Visual Studio Integrated Configuration Editor will adjust appropriately. Be warned, however, that any Enterprise Library Configuration Sections that had been previouly added will still be configured with the old settings and possibly cause you errors. Normally you make this switch before you add any Enterprise Library Configuration Sections / Application Blocks.
The dropdown list is populated from the Registry, which you can of course tinker yourself to make that dropdown list say anything you want:

If you choose a particular Enterprise Library Configuration Set, this will be stored in the .SLN file of your application:
GlobalSection(ExtensibilityGlobals) = postSolution
SelectedEnterpriseLibraryConfigurationSet = EntLib3Src
EndGlobalSection
Now that you know how to leverage a custom version of Enterprise Library in your applications, go customize :)