There are two ways to do things: one is to affect the entire image, and those options are under the Image menu. Things like Crop, Resize, etc affect all the layers.
The other is to affect just a layer or selected portion of a layer, and those are under the Edit menu. Things like Transform, Free Transform, Adjustments, etc.
Anything under the Image tab does the whole image, anything under the Edit tab does just the active layer. There's always a way to do something to just a layer rather than the whole image. No need to resize, rotate, crop, etc on a separate image. Use Transform, making selections, delete key, etc
Have fun! Can't wait to see what you're cooking up