If there is the need to edit layers later, saving the image in Photoshop format before flattening is a requirement. Once it is flattened and saved, there is no return by backstepping. Save As allows for changing the format to a JPEG, PICT, BMP, etc without losing the layered image. These are the basics, but there is much more to it than presented here. However, learning these basics goes a long ways to making the use of layers second nature to where it can be performed without a lot of stride breaking consideration.
Experience is the only teacher, and the experience is a fun one.
The best aspect of layers is that it allows for the blending of parts from many different graphic applications, greatly expanding the capability for expression and increasing the satisfaction gained from the digital graphic process. There is nothing quite like having all one's tools functioning together as one, and this is why Photoshop remains the industry standard for image editing.