If you're cutting to the music, I would first make some marks on the timeline (using the * key on the keypad). Render the music to RAM using the 0 key on the keypad first. Then hit the * key while you're playing the music back, to whatever rhythm fits the track.
Once you've got those marks and are happy with the way they fit the groove, make opacity keyframes for the on and off. Then drag those keyframes to where your marks are, making sure, of course, that they're on the graphics track you want to flash on and off. Preview, and once you're happy with them (you might want to make a couple of sets to fit different parts of the music cut), save them as an Animation Preset, then when you need them, just apply them to the opacity track of other graphics you need.
I'm new to after effects, so I edited my clip to my timeline in Premiere Pro, where my music is. I've been replacing each clip(s) needing animated "with an after effects composition," provided in Premiere. With no music in my after effects timeline, do I import the song and cut to it that way, or is there another way to do it... I can't seem to get my music to play in ae.
I remember the first time I got bit by that one in AE. It was years ago, but it's not an intuitive thing. You're probably using the spacebar to play your preview, but you have to hit the Zero key on the number pad to get a preview with audio (RAM Preview). Either that, or you can sometimes get odd results if your audio is an mp3.