You mentioned that you don't have any quilting thread. If you are machine quilting you don't need quilting thread. All purpose thread is fine. Quilting thread is used for hand quilting.
If you use one color on the top and another on the bottom do a test piece first to check your tension. When top and bottom thread is the same color it all blends together and so if your tension is off a little it doesn't show. If you're using black on the bottom and another color on the top the black might show through on the top if the tension isn't right.
If you're stitching in the ditch the stitching isn't going to show much if any so color isn't that important. The back will show however so more attention needs to be paid to that. How much do you want your quilting to show? If you do then use a contrasting thread. If not use matching to the fabric.