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Calibre and Calibre Portable can share libraries. Any library you want Calibre Portable to access should be in a subfolder of the Calibre Portable folder on your external HDD.
You may need to use the Switch Between Libraries feature in order to find the library in either Calibre or Calibre Portable.
Also, are you sure you even need Calibre Portable? I use it myself, but from your description it sounds like you think you need it in order to maintain multiple libraries. This is not the case. Regular Calibre can handle multiple libraries just fine.
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