Hello, this words are synonymous, but "comprender" Is more deep and is related to ideas, messages, emotions or feelings. For example: "Por lo que comprendí del texto, dice que no se debe juzgar a las personas". And "entender", is more rational and superficial. As the understanding, listening, or identify words. For example: "¡No entendí nada de lo que dijo; habla con un acento muy fuerte!. Jorge ;)

Hi, Geoff! Basically those two words mean the same thing. And "Cuál es la diferencia entre [X] y [Y]?" is the right form. James.