That makes sense, Heather!
I know some of our students use 3-ring binders to sort their paperwork for the course, while others might use simple pocket folders or even file folders. Personally, I would default first to whatever materials I had handy before buying something, but if you don't have anything at all handy or nothing that works well for you, you might just want to browse the stationary aisle at your most convenient store for some ideas there.
With a 3-ring binder, you can separate out sections as most make sense to you - by syllabus section, by type of assignment, or by deadline/month/week are the three that come to mind for me most readily - so that you can quickly flip to the labeled section you need to be in. Personally, I think I would sort all the readings into their own section at the front and then sort everything else after that first divider by deadline, printing out each deadline's worth of material as the deadline is assigned or placing new dividers as you go. The problem with sorting any printed readings into "deadline" or "syllabus section" areas in a notebook instead is that you may well forget to go back over them again later, and they really aren't meant to be read just once and then move on - we want you to refer to them as needed throughout the module.
It may even be worth having a small binder just for the readings and continuing to add to it (or replace repeated readings with an updated version, like the "Deadlines and Extensions" posts that change a little bit each module) as you go through the course. Then you could sort the readings out by other categories, such as course policies (like the deadline explanations), assignment instructions (like the final exam instructions in Modules I and II), or coding-specific readings (like the Neoplasms and Pregnancy explanations in Module I that continue to be helpful in Modules III and IV if you don't forget about them).
That said, I'm not necessarily advocating that you buy binders just for this! If you have file folders or pocket folders handy, they can be just as good at organizing your papers, you just need to label them clearly so you can go to the right folder easily when you need it. They won't hold as much as a binder, so you're more likely to put in a single folder the same sort of material you'd put in a single section within a binder if you're using dividers - this would be the "by deadline" or "by syllabus section" or "by assignment type" sorting. If you would put a divider in a binder just for the assignments in Section 5, you would use a folder just for Section 5 instead.
This is just how I would handle it, too - hopefully some students with different setups will chime in as well!
-Glenda