I too press mine open. One reason is because it is helpful when you snip the quilt because you butt up against your seam and it helps you avoid cutting into it.
You also have less bulk to cut through. Yes, you have to clip each side that way but, if you are using regular scissors (whether they are high quality or not) cutting through 4 layers of flannel, your hand is going to be hurting. If have Rag Quilting Snips (Olfa and Fiskars makes them), they are much easier on the hand and cut through the multiple layers very well.
Either way works. You will learn alot about what works for you on this first one. Then, you'll most likely change things for the next one!
Post a pic when you're done.