There are many ways to use an embroidery/sewing machine to quilt a quilt. I used to do the QAYG method similar to Rhonda K's post above. I usually do a combination of methods. I complete my quilt sandwich as usual. Then select a design that fits the blocks and style of the quilt. I use a free embroidery software program called 'My Editor' for any small modifications, information, and if necessary to convert the design file to the extension that is appropriate for my machine. (HV Topaz 20 will read VIP, VP3, HUS, and other file extensions). I load the file/files on my memory stick, insert it into my machine. I hoop the quilt sandwich. This for me is the hardest part. Getting the design centered in my block. Then load the hoop into the machine and stitch out the design. I often SITD or FMQ small portions of the quilt as well. There are quilting design files that are designed especially for borders and corners/setting triangles. And as summitbay said, you can also select quilting designs that you line up to do E2E designs. This is my method. I also use my machine to make 'in the hoop" ITH applique blocks. I completed a Baltimore album quilt using this method.
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The 9 patch quilt is an example of the process I use. I used a corner design for the setting triangles, a square design for the white blocks, and SITD for the 9 patch and rails. The last picture is of the Baltimore Album quilt done with In The Hoop embroidery designs, FMQ squares around the applique, and a quilting design on the borders. This was the 3rd quilt I completed, so it is a little more basic in the quilting as I was learning. It completed by making a quilt sandwich after each applique block was done, quilted, and joined to the next block using the sashing.
I love this process, and like any process, you get better as you learn, and find what works best for you. I love this method, although the machine, hoops, etc. are expensive to start. The quilting design patterns are not very expensive. Best of luck if you decide to give it a try.