I prefer spray basting because it holds the layers together better. I also like to heavily starch the backing before layering (and also spray starch the top) because starch stabilizes fabrics so they are less likely to stretch and create tucks and puckers while machine quilting.
With machine quilting you want to think about keeping starts and stops at the edges of the quilt if you design allows this. If I am doing lines, I will start in the middle of an edge and work my way to the opposite edge for the first line of stitching. If doing lines in both directions, my second line of stitching would be going the opposite direction -- again from edge to edge. This stabilizes the center. From there, I work out from the initial lines -- always starting and stopping at an edge. In other words, I make a big + or X first with quilting lines, then work out from those.