I noticed that this pattern is written so that you can work it from written instructions or from the chart. If you don't want to work from the chart you don't have to.
If you decide to use the charts (and charts are a good thing to learn and most people like them better than written directions once they become familiar with them--but not everyone) remember that the charts show the outside of the work.
TrikkeAddict, is right in what she said but I'll try to make it a little clearer. Each "no stitch" square is kind of a place holder for stitches that will be added later. If you counted the stitches at the bottom of the chart, skipping the dark gray squares you should find that they equal the amount cast on (when you add all the charts together). When you work across the chart just skip the gray squares. I know it seems confusing, but that is really the explanation. Work the white boxes up to the gray, then skip over the gray and start the next white boxes. Later they add stitches over the top of the gray columns and then there are stitches there, but for now they are not there.
Say you had 40 white squares to start with on the bottom row and 4 gray squares. You would start out with a cast on of 40, then at the top of each gray column it says to M1, now you have 42 white squares. But to keep the chart square when you are starting out then have to use place holders for those stitches or it would be hard to draw the chart.
Just skip over them and have faith.