You have so many questions and you haven't even started the quilt. That's funny to me. Okay, I haven't made a mason jar quilt but have made others. To decide my background colors, I look at the fabric colors I have and make sure I have a strong contrast.
When it comes to choosing thread color for the quilting, I will actually pull thread off the cone and lay it on the quilt to see if I like the color. I, also, consider what color the binding is going to be. Sometimes I use the same thread color as the binding to tie those two things together. All over quilting will be fine, but so would doing something special around or in the mason jars. Your long arm person can help you with those decisions.