Marcabas comes from the verb marcar (to mark). The imperfect tense here means it was a repeated action, so it translates to "you used to mark".
In the song, Ivan Cornejo sings, "¿Cómo olvidar los besos que me marcabas?" (How can I forget the kisses you used to mark me with?). He uses this beautiful metaphor to express how her kisses left a deep and permanent emotional imprint on him, making them impossible to forget.
This song is a classic sad-boy anthem about a breakup that's impossible to get over. Ivan Cornejo starts by telling us he fell for a woman who is "en verdad es peligrosa" [truly dangerous]. Why? Because "con su mirada muy fácilmente a todos enamora" [with her gaze, she very easily makes everyone fall in love]. He's not just another guy, though. He remembers the last time he saw her and "sentía mariposas" [felt butterflies]. He was completely hooked.
Now, he's trying to move on, but it's not working. He asks, "¿Cómo piensas que se me va a borrar tan fácil?" [How do you think it's going to be so easy for me to erase?]. He's stuck replaying memories of her kisses and the way she used to dance for him. Even though he knows their "cuento ya llegó a su fin" [story has reached its end], he can't let go. The song ends with him wishing her the best, "aunque no sea conmigo" [even if it's not with me], which is a really sweet but heartbreaking way to accept that it's over.