Hello Dave,
For polar aligning your mount, the recommended app is "SkEye Cam". It uses the phone's camera to recognize stars and guide the alignment. And it doesn't need Polaris to be visible.
For polar alignment, you can affix the phone on the OTA in any convenient orientation, as long as the camera points towards the sky (preferably midway between zenith and celestial equator).
The other apps, SkEye and SkEye Pro, do not support polar alignment at the moment. They are mainly for PushTo navigation to help visual observation. (Though, I hope to integrate the apps together eventually). They may yet be used for rough polar alignment with the help of a polar scope, but that requires visibility of Polaris.
Please let me know if you have any other questions,
Harshad