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I create a Houdini project with all it's folders right inside my Assets folder in my Unity project.

Projectception works fine, and then I just use any .HDA directly from my hda folder and if I need to test something I just put it on the geo or text folders.

So I have both Unity and Houdini open and save the tool in Houdini and see the changes immediately in Unity.

I have never had any problem with that workflow, and I can even have my Houdini files synced with my repository.

You can also set the $HOUDINI_PATH environment variables prior to launching Unity and Houdini in a shell such as a batch script. This is what is normally done in a production environment. However, in the case of the houdinijam the method provide is the simplest and straight forward approach.