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.