Often there's no one-to-one correspondence between expressions in one language and another. But once you've seen enough examples of actual use, you'll get a good idea of the nuances.
"Sich merken" is closer to "to remember".
"Sich einprägen" means something like "to remember strongly". "Prägen" means "to stamp, to emboss", so the image is "to stamp something into your memory, like one would stamp a picture on a coin".
For "to memorize a list of words", I'd use "eine Liste von Worten/Vokabeln (auswendig) lernen", i.e. "to learn (by heart)".