I have used invisible thread only on wallhangings that will never be washed. I made some quilts with hand embroidered centers and used it to quilt over the embroidery. If I don't do that, it looks bulky. Other than that I don't use it for much. As of which thread to use for quilting, also depends on the quilt. If the quilt will be washed often and used daily, I will use 40 wt on the top and bottom. For a fancy wallhanging, I will use thread as fine as 60 wt for the top and bottom. About colors, this time it depends on what you want your quilt to look like. Sometimes I want my quilting to show. This is not well accomplished in a quilt that has many colors and printed fabrics. You do this better with mild prints and solid colors, and you can use a shinny thread or a very contrasting one. If you want your piecing to show more, use a more muted tone for the quilting. If possible, then change colors when changing the area of the quilt, but make sure your stitches are well anchored at the start and end of each color, and be very careful if jumping from one area to another. I only do this if my quilt is basted or heavily pinned. I don't like basting or pinning, so I mainly stitch adjacent areas rather than jumping around, even if that means frequent color changes.
Hope this helps.
Maria