Well, in the case of Autumn Rose, grey and white charts.....I'm with you Deb, I knit two handed fair isle (background with the right and pattern with the left hand) and I had trouble with this chart too when I started out.
I usually convert my charts into strictly black/white -- get rid of all of the symbols or the coloured charts that are hard to tell when a shade changes - and do exactly what you see in the SS4 book -- black and white chart with columns to the right and mark out which shade is used in which hand on each row.
Background yarn in the right (white boxes) and pattern yarn (grey boxes) in the left. Then it struck me -- the columns on this chart are reversed -- the white boxes are the left column and the grey boxes are the right column.....could it be something this simple that has our brains confused? It's early, maybe this is just too easy a solution, but if I had recognized this before I knit Autumn Rose, I would have changed this to make it more knitter friendly (for me).
I also did use markers to identify where each repeat was....and marked the chart accordingly - it made it much easier.
Don't put a marker before your side seam purl stitch, just put one after it -- you'll feel the marker, pull your yarn to the front, purl the stitch, put the yarn to the back, slip the marker and continue knitting.
Like anything else, it takes a while for your hands, eyes and brain to all get coordinated when starting a new project.