If you're making a big batch for the freezer, assemble them all before you start cooking them. I find it easiest to make them on one tortilla that you fold in half (see photo below for an example). Stuff them with your chosen filling and shredded cheese.
I find that the easiest and fastest way, by far, to cook quesadillas is on a panini press. If you don't own one, you can fry your quesadillas in a dry frying pan (if you like them soft) or an oiled frying pan (if you like them crispy) over low heat, flipping carefully half way though. I've read that you can also cook them in the oven, but to be honest I've never tried it!
If you're planning to freeze them, let them cool completely and then wrap them individually in plastic wrap like saran wrap and store in a large zip-top bag. You can thaw them in the microwave, oven or at room temperature. Then warm them and serve with salsa, sour cream (or plain yogurt, in our case!), and mashed avocado/guacamole. Enjoy! :)