Safety pins are not as good as thread basting for hand quilting. When thread basting, it is a good idea not to do a simple straight stitch, but rather do more of a herringbone stitch or tailor's stitch. This stitch is better at keeping the layers from shifting. Sharon Schamber has some good videos on Youtube about how to use this type of stitch to baste a quilt, even if you do not use other elements of her basting method. Here are links to her videos:
http://www.youtube.com/watch?v=bhwNylePFAA
http://www.youtube.com/watch?v=k_EjBGz5vGQ
I think it is in that second video where she shows the stitch.
When quilting with a hoop, it is a common beginner's mistake to make the quilt drum-tight. It should actually be quite loose. You should be able to move the quilt about 4 to 6 inches away from the hoop in either direction. When I took a class in hand quilting, the instructor recommended using your fist to measure this looseness. You want about a fist's distance in both directions at the center. This looseness allows you to manipulate the quilt onto the needle almost as if you were quilting without a hoop at all.
When using a hoop, you do want to be careful when re-hooping not to distort the layers of the basted quilt. The easiest way to do this is to thread baste with a Sharon Schamber type stitch. Once you have an area hooped, you can snip basting threads in the area you are quilting. Meanwhile, though, the stitches in the other areas are of a type that ensures against the layers shifting on you.