Depending upon the various layouts of your current LibGuide pages, content will be transferred over to the side-nav format in various ways. For instance,
if you switch from a tabbed navigation layout with 3 columns to the side-nav layout, the boxes from columns 2 and 3 will be moved to the bottom of the new column 1;
if you switch from a tabbed navigation layout with 2 columns to side-nav layout, the boxes from columns 1 and 2 should remain in the same position in the new layout.
Box / Content / Pages can be moved around / adjusted via the Pages tool at the top: