Josieh, are you talking about using a walking foot or FMQ? It makes a difference. I don't know how you could possibly sew in 2 different directions with the walking foot, while moving from the center to the edge, unless you were sewing in reverse, which is pretty hard to see. What I think you're asking is whether or not it matters that you will be going in the opposite direction on the second half, once you go back to the center and start moving toward the edge. If that's it, I don't see how you could avoid it without having over half of the quilt to your right on every other row.
Unless I'm misunderstanding this.
hugs,
Charlotte