One good way to practice with a metronome is to make it count longer beats as you get better at the song you are learning. Like, first have it count quarter notes. Then after a while half notes. Then whole notes. That way, you get used to counting the beats in your head and not always relying on the metronome to count every beat for you. If i'm not mistaken, I believe I saw this method on a Victor Wooten video a while back.