Where are files saved and why are they flattened

I'm new to Photoshop and Lightroom on my iPhone but a long time user of both on my computer. The most surpising thing to me is that I can save the file I am working on but it saves mysteriously never telling me where it is saved. When I try to open the original file I was working on I only see 'flattened' versions in my photos but the originals with layers I wanted to work with are gone. Can I have some insight into how this works as on the computer I always know where my files are. TIA,  Ken