There is a thread that is washable that I used in my bobbin for when I did trapunto. I usually SITD and then marked my quilts with stencils for my FMQ. I have preferred the look of SITD over just plain meandering. It just depends on the look of what you want your quilt to have. There is no law stating that you have to ditch your quilt, just do what you think looks best for your quilt. And enjoy the process.
I also would highly recommend you get your hands on the book "Heirloom Machine Quilting" by Harriett Hargrave. I learn my skills from taking a class with her. I was so lucky to have won some top awards with my quilting.