Register the custom tool DLL either in the Visual Studio local registry or in the system registry, under HKEY_CLASSES_ROOT.
For example, here's the registration information for the managed MSDataSetGenerator custom tool, which comes with Visual Studio:
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\VisualStudio\8.0\CLSID\{E76D53CC-3D4F-40A2-BD4D-4F3419755476}]
@="COM+ class: Microsoft.VSDesigner.CodeGenerator.TypedDataSourceGenerator.DataSourceGeneratorWrapper"
"InprocServer32"="C:\\WINDOWS\\system32\\mscoree.dll"
"ThreadingModel"="Both"
"Class"="Microsoft.VSDesigner.CodeGenerator.TypedDataSourceGenerator.DataSourceGeneratorWrapper"
"Assembly"="Microsoft.VSDesigner, Version=8.0.1200.0, Culture=Neutral, PublicKeyToken=b03f5f7f11d50a3a"