As a work written in hypertext, Shelley Jackson's Patchwork Girl is made up of links as well as lexias (substantially more links than lexias, in fact). It is the presence (and, in some cases, the absence) of links that make Patchwork Girl a "patchwork".
Patchwork, in its traditional sense, is the creation of a work (a quilt, for example) by sewing together scraps of fabric to create a sort of fabric mosaic (or, in the case of the Frankenstein story it parallels, sewing together scraps of people). Like a mosaic, it is the overall effect of the work that is important; the viewer who is captivated by any given patch to the point of exclusion of the rest is missing the point, just as the reader who focuses on a single narrative thread of Jackson's work (though her prose is far more captivating than any scrap of cloth) fails to get the full effect.
The difficulty of "getting the point" of Patchwork Girl lies in the fact that, unlike when viewing a quilt, one cannot step back from the screen to see the work in full. The only views the reader is allowed are a close-up of a few lexias at a time (due to limitations of RAM and resolution) or an overview mode that shows structure but little content (a view analogous even in appearance to a paint-by-number picture). Since the emphasized view is that which focuses on the individual lexia, the "needlework" of connecting the lexia takes on the importance of guiding the eye (and mind) through the work.