Her books go back and forth between modern time and the Civil War era. The characters in the Civil War era books are relatives of Sylvia's.
This link shows the order the books were written if you scroll down and read back up from the Quilter's Apprentice. If you notice some of the titles are actually 2 - 3 of the books put together under one title, so you won't need to read those.
The Runaway Quilt, The Sugar Camp Quilt, The Lost Quilter and the Union Quilters are historical and do not have to be read in order with the modern ones if you don't want to do so.
http://elmcreek.net/books