Layer alignment questions after creating a stack

[JerryandLoisPhotography]

Hello,

I'm trying to learn the finer nuances of creating a stack, with layer alignhment enabled.

I just created a stack of 50 images. Most were perfectly aligned before creating the stack, as these were shot when the camera was in its final position. the first set of images were shot when I was adjusting the camera position, looking for the right sweet spot.

After stacking with attempted alignment enabled, there's one layer that's off a good 50 pixels or so.

While I can manually nudge it into place, I would prefer to have PS do this for me.  

Is there a way to "declare" or somehow tag which layer is the reference point in PS, and force the non-aligned layer to conform to the reference layer?

The reason for asking: 50 layers was a test case/proof of concept. My real data set is around 160 files, of which some 30 or so are not aligned due to me seeking the sweet spot to shoot everything (i.e. adjusting the camera position on the tripod).

Working in the most current PS beta in Win10/64 (also current).

Thanks!!!!!

[JerryandLoisPhotography]

Additional info:
I locked one layer (apparently this turns it into a reference layer as I was hoping).  I then selected the misaligned layer and the locked layer.

With both layers visible and enabled, I opened the edit menu.  Align Layers is greyed out.

Not sure how to proceed...

Thanks again!