When you use an art program (I use FireAlpaca which is great and free :3) you can draw things on different "layers" which lets you i color take on and off while everything else is there. So like when I'm using a base, I draw over it instead of with it. So when I color, I go between those layers so i don't have to erase anything :3
or if you don't like something you can take it off and draw it again without the rest of your art being affected.
Sorry, I hope that wasn't too confusing xP

TL;DR: It's not all one piece like a png or jpeg would be :3