A few things that are important when you use it:
1) Always say the word at the same time as you sign it. It forms a good association between word and sign.

2) Speak in full sentences. You might only be signing one or two words in the sentence, but it's still important to model those whole sentences. (This also goes for speaking without Makaton. Nothing annoys me more than people who underestimate their kids' intellect and use baby talk) If you need to repeat a sign, you can repeat just the word and sign.

3) Use whatever signs are appropriate to you. If your child doesn't eat toast, then there's not much point using the sign for toast etc

Good luck - I think it's a wonderful system. And no, 3 is not too late. What's the worst that can happen - it doesn't work? You wouldn't be any worse off...