crop photo not layer

I'm new to photoshop and am trying to create an image involving an uploaded photo overlaid on another image (a template someone gave me) so that my photo fits inside a part of the template. I have imported my photo as a second layer but I need to tweak the relative dimensions of the photo to make it fit. Every attempt I make to crop the photo to the new dimensions results in the layer getting cropped not the photo. This is maddening. I can adjust the size and rotation of the photo fine, but the crop tool seems to apply only to the layer not to the photo itself. If I do crop the photo layer, it affects the template layer too. This is maddening. Is there a function I havent found yet or am I misunderstanding  something fundamental about how PS works?!