Your projects will instantiate the automapped plug as long as it's the only One with that vst-id in your scan path.
As I said, I don't rely on the hosts behaviour scanning multiple plugs with the Same vst-id. Every Host behaves different. Sonar x1 lists both in its ui, but instantiated only the first scanned, and x1 sorts multiple Plugin paths alphabetically, which influences the scan order... Cubase lists both vst2.4 when the dll name length is shorter than 9 chars, the automap ones otherwise but can't find a plugs preset anymore then, when the dll name differs from the dll name the presets were made with...
I advice to copy the Vst2 dlls to their own folder structure, so that these are singletons VST-id wise...