It depends here on the actual emotion itself, but as I mentioned a few days ago we want to try to balance the Compassion and Lovingkindness meditation similar to when we see the kid falling off the bicycle. Try not to go into grief, anger, fear, whatever. Try not to get too high in "Metta." We do want to balance it. As the meditation develops, and the more wisdom you have, then the meditation itself will become balanced and the emotions will gradually lessen in their intensity. Then at times depending on the emotion, if it comes up, you might just note it, it's a distraction, and you come back to the meditation. If it's a very intense emotion then normally it's going to indicate that you're going off balance in the meditation itself. So you might want to recollect that so you'll remember how your meditation is to be done in a more balanced way. If you are confused ask a teacher or another good wise spiritual friend.