Is it possible that you're working from an uncorrected copy of the pattern? I just followed the link you provided to Ravelry and found this paragraph:
"Thanks to a knitalong with the Hat of the Month group here on Rav, errors and confusing bits in the ha pattern have now been corrected, and the written pattern should be in good shape."
Also, even though I'm just beginning my knitting life, I'm using differently colored stitch markers all over the place to "mean" different things: long cast-ons, to help keep my count; charted pattern repeats (of course); beginning of a row in the round. And that's just the first couple of projects/classes. I also use markers to let me know how far, literally, a skein of yarn goes in a multi-skein project.
So...maybe there are corrections available since the version you have was produced? And maybe LOTS of nice, differently colored stitch markers would help?
My Waterloo so far is not being able to say NO to anything, unless it's absolutely so complicated that there's just no way I'll be able to do it in the foreseeable future.