My first quilting system was the same one you have, and I did almost all my quilting freehanded, usually allovers. For actual designs, as you mention, I eyeballed the space that I wanted the design in, and made the design in my mind fit the space.
I also liked to have a drawn or printed image of that design pinned up on the wall where I could see it from my quilting position at the frame, that often helps tremendously.
The advice I've seen from professionals say to practice drawing out on paper what you want to stitch - the drawing practice will translate well when you go to stitch at the machine.
I also started printing out designs of thin paper and pinning or gluesticking the paper on the quilt where I wanted to stitch, then stitch through the paper and tear it away after.
But I always like freehand best I guess.