To "heat ___ up" means to make something warm enough to use. You "heat up" cold food or a cold room:

It's freezing in here! Do you want to turn the heater on and heat it up?

The word "heat" by itself also means to make something warm, but it sounds a little too technical to use when you're speaking conversationally about food. However, it's perfect to use for a written recipe:

Heat the oil in a large skillet over medium heat; add the onions and cook until brown.